towhee-users — Informs users who opt-in about significant bugs and new features

[Towhee-users] aqueous solution

[ho t. <hoa...@ya...>]

Dear Towhee users and developers,

I am Tuan Ho, from Sandia National Labs.
I have a question regarding scaling the box in NPT simulation of aqueous solution.

I am trying to study solubility of CO2 in NaCl solution. I used NPT with two boxes. First, I created a box of CO2 (box 2), and a box of NaCl+Water (box1). Then I equilibrated these two boxes to the right condition of temperature and pressure. For CO2 box it is very fast to scale the box to the right box volume corresponding to T, P. But for water+ NaCl box, it took me months.  Anyone has experience on this simulation or know how to speed up the simulation please let me know.


This is the probability I used in my simulation (I don't allow the swap between two boxes yet)
pmvol     
0.8d0   
          pmvlpr
          0.9d0 1.0d0
          rmvol
          1.0d0
          tavol
          0.5d0
pm1boxcbswap
0.9d0
          pm1cbswmt
          0.2d0 0.0d0 0.6 1.0 
pmtracm
0.950d0
          pmtcmt
          0.3d0 0.0 0.65 1.0d0      	
          rmtrac
          1.5d0 
          tatrac
          0.8d0
pmrotate
1.0d0
          pmromt  
          1.0d0  1.0d0 1.0 1.0
          rmrot
          0.05d0
          tarot
          0.5d0


Thank you very much.

Tuan

[Towhee-users] GCMC calculation to find solubility of water in dodecane

[Pragati A S. <pa....@nc...>]

Hi,
I want to calculate solubility of water in dodecane by GCMC calculations using towhee. I already have pdb file for equilibrated box of Dodecane containing 216 chains, generated using Gromacs code. I want to use the same pdb in towhee. So I converted pdb to towhee_coords, used initstyle='coords'.  But the output pdb is generated for only 1 chain (nmolectyp =1 ). Why it is not taking coordinates for all the 216 chains (nmolectyp = 216) from towhee_coords and generating output  pdb file.

My Towhee_input file for GCMC calculation looks like:
inputformat
'Towhee'
ensemble
'uvt'
temperature
300.0d0
nmolty
2
nmolectyp
216  1
chempot
0.0  730.0d0
numboxes
1
stepstyle
'moves'
nstep
100
printfreq
10
blocksize
20
moviefreq
1000
backupfreq
1000'internal'
ffnumber
1
ff_filename
/data/home/psharma/monte-carlo/towhee-7.1.0/ForceFields/towhee_ff_Charmm27
classical_potential
'Lennard-Jones'
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.false.
rmin
1.0d0
rcut
12.00d0
rcutin
5.0d0
electrostatic_form
'coulomb'
coulombstyle
'ewald_fixed_kmax'
kalp
5.6d0
kmax
5
dielect
1.0d0
linit
T
initboxtype
'dimensions'
runoutput
'full'
pdb_output_freq
100
pressurefreq
20
trmaxdispfreq
1000
volmaxdispfreq
1000
potentialstyle
'internal'
ffnumber
1
ff_filename
/towheebase/towhee-7.1.0/ForceFields/towhee_ff_Charmm27
classical_potential
'Lennard-Jones'
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.false.
rmin
1.0d0
rcut
12.00d0
rcutin
5.0d0
electrostatic_form
'coulomb'
coulombstyle
'ewald_fixed_kmax'
kalp
5.6d0
kmax
5
dielect
1.0d0
linit
T
initboxtype
'dimensions'
initstyle
'coords' 'full cbmc'
initlattice
'simple cubic' 'simple cubic'
initmol
216  0
inix iniy iniz
6 6 6
hmatrix
43.2d0 0.0d0 0.0d0
0.0d0   43.2d0  0.0d0
0.0d0 0.0d0  43.2d0
pmuvtcbswap
0.25d0
          pmuvtcbmt
          0.0d0 1.0d0
pm1boxcbswap
0.0d0
          pm1cbswmt
          0.0d0 1.0d0
pmavb1
0.0d0
          pmavb1in
          0.5d0
          pmavb1mt
          1.0d0 1.0d0
          pmavb1ct
          1.0d0 1.0d0
          1.0d0 1.0d0
          avb1rad
          5.0d0
pmavb2
0.0d0
          pmavb2in
          0.5
          pmavb2mt
          1.0d0 1.0d0
          pmavb2ct
          1.0d0 1.0d0

 1.0d0 1.0d0
          avb2rad
          5.0d0
pmavb3
0.0d0
          pmavb3mt
          1.0d0 1.0d0
          pmavb3ct
          1.0d0 1.0d0
          1.0d0 1.0d0
          avb3rad
          5.0d0
pmcb
0.50d0
          pmcbmt
          0.0d0 1.0d0
          pmall
          0.0d0 0.0d0
pmback
0.0d0
          pmbkmt
          0.0d0 1.0d0
pmpivot
0.0d0
          pmpivmt
          0.0d0 1.0d0
pmconrot
0.0d0
          pmcrmt
          0.0d0 1.0d0
pmcrback
0.0d0
          pmcrbmt
          0.0d0 1.0d0
pmplane
0.0d0
 pmplanebox
          1.0d0
          planewidth
          3.0d0
pmrow
0.0d0
          pmrowbox
          1.0d0
          rowwidth
          3.0d0
pmtraat
0.0d0
          pmtamt
          1.0d0 0.0d0
          rmtraa
          0.5d0
          tatraa
          0.5d0
pmtracm
0.75d0
          pmtcmt
          0.1d0 1.0d0
          rmtrac
          0.5d0
          tatrac
          0.5d0
pmrotate
1.0d0
          pmromt
          0.1d0 1.0d0
          rmrot
          0.05d0
          tarot
 0.5d0
cbmc_formulation
'Martin and Siepmann 1999 + Martin and Thompson 2004'
cbmc_setting_style
'default ideal'
#polymer
input_style
'basic connectivity map'
nunit
38
nmaxcbmc
38
lpdbnames
F
forcefield
'Charmm27'
charge_assignment
'none'
unit ntype
1 'CTL3'
vibration
4
2 3 4 5
improper torsion
0
unit ntype
2 'HAL3'
vibration
1
1improper torsion
0
unit ntype
4 'HAL3'
vibration
1
1
improper torsion
0
unit ntype
5 'CTL2'
vibration
4
1 6 7 8
improper torsion
0
unit ntype
6 'HAL2'
vibration
1
5
improper torsion
0
unit ntype
7 'HAL2'
vibration
1
5
improper torsion
0
unit ntype
8  'CTL2'
vibration
4
5 9 10 11
improper torsion
0
unit ntype
9 'HAL2'
vibration
1
8
improper torsion
0
unit ntype
10 'HAL2'
vibration
1
8
improper torsion
0
unit ntype
11 'CTL2'
vibration
4
8 12 13 14
improper torsion
0
unit ntype
12 'HAL2'
vibration
1
11
improper torsion
0
unit ntype
13 'HAL2'
vibration
1
11
improper torsion
0
unit ntype
14 'CTL2'
vibration
4
11 15 16 17
improper torsion
0
unit ntype
15 'HAL2'
vibration
1
14
improper torsion
0
unit ntype
16 'HAL2'
vibration
1
14
improper torsion
0
unit ntype
17 'CTL2'
vibration
4
14 18 19 20
improper torsion
0
unit ntype

18 'HAL2'
vibration
1
17
improper torsion
0
unit ntype
19 'HAL2'
vibration
1
17
improper torsion
0
unit ntype
20 'CTL2'
vibration
4
17 21 22 23
improper torsion
0
unit ntype
21 'HAL2'
vibration
1
20
improper torsion
0
unit ntype
22 'HAL2'
vibration
1
20
improper torsion
0
unit ntype
23 'CTL2'
vibration
4
20 24 25 26
improper torsion
0
unit ntype
24 'HAL2'
vibration
1
23
improper torsion
0
unit ntype
25 'HAL2'
vibration
1
23
improper torsion
0
unit ntype
26 'CTL2'
vibration
4
23 27 28 29
improper torsion
0
unit ntype
27 'HAL2'
vibration
1
26
improper torsion
0
unit ntype
28 'HAL2'
vibration
1
26
improper torsion
0
unit ntype
29 'CTL2'
vibration
4
26 30 31 32
improper torsion
0
unit ntype
30 'HAL2'
vibration
1
29
improper torsion
0
unit ntype
31 'HAL2'
vibration
1
29
improper torsion

0
unit ntype
32 'CTL2'
vibration
4
29 33 34 35
improper torsion
0
unit ntype
33 'HAL2'
vibration
1
32
improper torsion
0
unit ntype
34 'HAL2'
vibration
1
32
improper torsion
0
unit ntype
35 'CTL3'
vibration
4
32 36 37 38
improper torsion
0
unit ntype
36 'HAL3'
vibration
1
35
improper torsion
0

unit ntype
37 'HAL3'
vibration
1
35
improper torsion
0
unit ntype
38 'HAL3'
vibration
1
35
improper torsion
0
#water
input_style
'basic connectivity map'
nunit
3
nmaxcbmc
3
lpdbnames
F
forcefield
'Charmm27'
charge_assignment
'none'
unit ntype
1 'HT'
vibration
1
2
improper
0
unit ntype
2 'OT'

vibration
2
1 3
improper
0
unit ntype
3 'HT'
vibration
1
2
improper
0

Can anybody help me out, how to solve this problem.
Thanks

________________________________

Disclaimer:

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[Towhee-users] viewing simulation trajectory

[Chandan C. <ii...@gm...>]

Dear Towhee users,

I have just started using Towhee and trying out the examples.
Can someone point me how do I view the simulation trajectories
(towhee_movie) for NPT and uVT ensembles.

Thanks

Chandan

-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*

[Towhee-users] Problem with Cylopentane

[<doe...@po...>]

Dear towhee-users, dear Marcus,

I'm quite new to towhee and have problems with Cylopentane
in the NpT-ensemble.  I want to use the Trappe-UA Potential with 
paramters
taken from the Siepman page 
(http://www.chem.umn.edu/groups/siepmann/trappe/molname.php).
Since I didn't find the parameters in the regular towhee_ff_TraPPE-UA 
file, I created a force-field
file on my own. Unfortunately I get the following error, when I start 
the simulation:

INITCONF: building template for molecule type:    1
Initial Structure Growth Trial:    1
  unable to generate an initial conformation
  molecule type            1
  READTOWHEE: there was an error in initconf

I attached my input and force field file ( called ff).

I would be very happy, if anybody could give me some advice.
Thank you very much for your effort in advance.

Best regards
Mark

[Towhee-users] Volume Change for Gibbs Ensemble

[Maytham Al I. <ma...@st...>]

Dear all,

 

I'm conducting molecular simulations to determine VLE for methane inside
graphitic slit pores. The ensemble is nvt with 2 boxes. Each box is a slit
pore. How can I perform a volume exchange between the two boxes
anisotropically? For example, if I change hmatrix in x-direction of one box
by let's say +1 angstrom, I want to change the same hmatrix (i.e. in
x-direction) of the other box by -1 angstrom. 

 

pmcell is used for anisotropic volume move. However, the volume of one box
is changed anisotropically, but the volume of the second box is changed
isotropically. Is there a way to ask the molecular simulator to conduct
anisotropic volume changes for both boxes?

 

Thank you,

Maytham

[Towhee-users] General questions about Towhee program

[Jianying Hu <jx...@ca...>]

Dear Friends,

Recently I am learning Towhee and have some questions:

1) I have PDB file of a molecule. Can I use pdb file directly or need I
convert pdb to towhee_coords file? And how to convert?

2) For invib, do I need to list all atoms following the pdb file? Or I only
list different types of atoms?

3) For ijvib, I did not figure out the meaning of each number?

4) In the examples, I saw 'd0' in some items, like 'kalp 5.6d0'. I thought
the unit is Angstrom.

5) How to consider a system containing different molecules?

6) Finally, in my system, there is no solvent. What value should be for
'dielect'?


Thank you so much in advance!

Jane

Case Western Reserve University
2104 Adelbert RD, Bingham Building 203C
Cleveland, OH 44106
E-mail: jx...@ca...

[Towhee-users] Is towhee suitable to simulate sheet molecules

[Salomon T. C. <stu...@gm...>]

Hey Marcus,

I want to perform simulations of the model described in this paper:

http://pubs.acs.org/doi/abs/10.1021/ma902081m

I remember in my previous work with towhee that it had issues if there
where rings within a molecule's topology. Will towhee be able to work with
such a model with 2D bond connectivity?

-s-

-- 
Salomon Turgman Cohen
Assistant Professor
Chemical Engineering
Kettering University
(919) 341-9650

[Towhee-users] histogram reweighting

[mehdi n. <moh...@gm...>]

Hi Dear all
Happy New Year
I would like to calculate coexistence properties of binary mixture by
grand canonical ensemble using histogram reweighting and I have some
questions:
- Which role does the "midpt&slope" in "file_phase" play? and how we
can determine the accurate value of them?
- In lower temperature how we can determine the number of initial
molecules in system?
- How we can calculate the critical properties of system by analyse_histogram?

[Towhee-users] (no subject)

[mehdi n. <moh...@gm...>]

moh...@gm...

[Towhee-users] histogram reweighting

[mm n <moh...@gm...>]

Hi Dear all
Happy New Year
I would like to calculate coexistence properties of binary mixture by
grand canonical ensemble using histogram reweighting and I have some
questions:
- Which role does the "midpt&slope" in "file_phase" play? and how we
can determine the accurate value of them?
- In lower temperature how we can determine the number of initial
molecules in system?
- How we can calculate the critical properties of system by analyse_histogram?

[Towhee-users] Compilation of utility programs

[pascal b. <pas...@un...>]

Dear all,

I have solved the problem by compiling with gfortran and gcc. Obviously 
the combination ifort+icc does not work.

Pascal

[Towhee-users] compilation problem

[pascal b. <pas...@un...>]

Dear all,

I am using towhee 7.1.0. I have compiled it with ifort in serial version 
without problems.

Now, I am trying to compile the utility programs but it fails with the 
error message:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status

Does anyone have seen this before and know how to fix it?

Thank you in advance
Best regards
Pascal

Re: [Towhee-users] VOLNPT output: an error message?

[Jure V. <jur...@ki...>]

Dear Marcus and Aric,

I have a related situation: I wish to simulate adsorption in a non-rigid 
crystal framework, which of course runs into the VOLNPT limitation.

> Indeed the error messages do mean there is a problem.  When you perform a
> volume move in Towhee it scales the center of mass position of all the
> molecules (in a manner appropriate for the volume change) and then keeps
> all of the intramolecular distances the same.  This is not possible when
> the "molecule" spans the periodic images with its bonding pattern.
> 
> You would need a completely different move that scaled the intramolecular
> distances for the volume change.  That would then lead to problems with any
> molecule that has a rigid bond length (as the attempt to change that bond
> length would result in an infinite energy) and also would be fairly
> inefficient as the intramolecular distances are quite sensitive.

I have been considering implementing this for towhee. Our material undergoes 
non-negligible changes in unit cell shape, so inefficiency is what we have to 
live with. Rigid bonds would remain forbidden, you can't have it both ways. 
Marcus, are you aware of any other limitations in towhee that I need to be 
aware of before I attempt this? Any advice?

Regards
Jure Varlec

Re: [Towhee-users] VOLNPT output: an error message?

[Aric N. <agn...@en...>]

Dear Marcus and Mike,

I have had a second day to think over both or your comments and I believe that (perhaps) all has been illuminated.  I provide this follow-up reply for the discussion board and future users who may need to search the knowledge base in the future.

If I understand correctly:

1) bonds across the periodic boundaries are in violation of the VOLNPT.f because a cross-boundary bond cannot maintain a constant interatomic distance between two atoms with a volume change in the simulation cell.

and

2)  the VOLNPT move scales the position of the center of mass of the molecule with respect to the volume change and leaves the interatomic positions unchanged.  

These two points are related, but with respect to the montmorillonite sheets, if each sheet is defined as a molecule with bonds across the boundaries, then it violates 1) and 2) above because of the bonds.  

I have simulated each montmorillonite sheet without bonds (that is how the non-bonded CLAYFF forcefield intends) but received a line in the towhee_output that reads, “unit 2 not connected via bonding graph to atom 1 therefore MC moves will not be allowed to alter atom positions for this molecule”.  This output was the reason for creating the model with bonds that violates 1) and 2) above.  However, even if I could move each nonbonded montmorillonite sheet as a molecule, I would still have issues with VOLNPT.f because it adjusts the center of mass of the molecule while maintaining the interatomic distances in the molecule (i.e. cracks/ gaps would develop at the boundaries of the simulation cell with each pmcell move because the interatomic distances are unchanged).

If I define each atom in the montmorillonite sheet as a molecule (as Marcus suggested), then the VOLNPT.f will adjust/scale the position of each atom/ molecule with each pmcell move and “fill” the simulation cell as the atom/molecule positions are scaled based on their center-of mass  (and the montmorllonite relaxes).  This simulation approach with each atom as a molecule is the closest to the simulation design that I am trying to execute, but I will have to accept a much more rigid montmorillonite framework and the density fluctuations.

Other MD-NPT simulations of phyllosilicates (including montmorillonite) and CLAYFF have provided reasonable experimental data for the mineral unit cell parameters, interlayer d-spacing, and density [Cygan et al. 2004, J. Phys. Chem B. 108(4)].  Is there something about the anisotropic NPT MC algorithm that I am overlooking that is going to result in density fluctuations that are significantly greater than in previous anisotropic MD-NPT simulations?  I don’t expect the simulation cell size to diverge significantly from the equilibrium values as determined via MD.  Is this an unrealistic expectation?

Thank you,

Aric Newton



On Oct 6, 2014, at 4:35 PM, Aric Newton <agn...@en...> wrote:

> Dear Marcus,
> 
> Thank you for your reply.  I understand that the errant output is a result of the model violating the constraints of the pmcell move by having bonds in each montmorillonite layer that cross the boundary.  The harmonic bonds that cross the boundary have spring constants of zero.  Thus, the energy of these bonds is independent of the positions of the atoms (i.e. it’s always zero).  This condition is a result of the parameters in the CLAYFF forcefield.  I have only “created” these bonds because I would like each montmorillonite layer to be able to translate (as a unit)  in the x-, y-, or z-direction as part of the MC moves.
> 
> I can create an input file without these zero-force constant “bonds”, in which case each atom in the montmorillonite is a molecule, but I have been unable to group these individual molecules into a super-molecule that I can then translate as a unit.  My starting simulation cell size is the equilibrium cell size from a 1.0 ns MD-NPT in LAMMPS, so I am not too worried about the changes in the MMT density.  With an anisotropic MC-NPT that only has a five percent probability of performing a pmcell move, I suspect that density fluctuations in the montmorillonite should be limited and, I am assuming, negligible.  Is this a reasonable assumption?
> 
> These simulations are part of a thermodynamic integration.  The model has only one box and the equilibrium cell parameters from the MD-NPT simulation confirm that my layer spacing and water content are consistent with the experimental condition that I am trying to simulate.  So, if the pmcell move adjusts the center of mass of each atom in the montmorillonite sheets in a manner appropriate with the volume change (adjusting interatomic distances), then that is what I want.  However, is there a way to also get the center of mass of each sheet to translate as part of the pmtracm command when in fact each sheet is composed of many molecules?  The pmplane move sounds close to what I want, but I am unsure how to define a dynamic definition of the plane so that it always includes only a montmorillonite sheet regardless of previous translation moves during the simulation. Do you have any suggestions or is simulating with rigid montmorillonite layers the only option with the current move algorithms?
> 
> Thank you,
> 
> Aric Newton
> 
> 
> On Oct 6, 2014, at 10:02 AM, Marcus Martin <me...@gm...> wrote:
> 
>> On Fri, Oct 3, 2014 at 4:22 AM, Aric Newton <agn...@en...> wrote:
>> 
>> I am using towhee for a one box MC-NPT simulation of two montmorillonite layers with an interlayer space containing the counter ions and water molecules.  Each montmorillonite layer is treated as an individual molecule and moves as a unit via the pmtracm move probability.  I have previously equilibrated the system at high temperature in the NVT ensemble without any errors, but the output that I am getting now that I have switched to the NPT ensemble leaves me a bit uncertain.  In the towhee_output file, there are about 10,000 lines that read as below.   
>> 
>>  VOLNPT: move attemped in box that has a periodic bonded molecule
>>  Molecule type:      -31414
>>  Chain number:           1
>>  Box:           2
>> ...
>> 
>> The *.pdb snapshots are being output during the simulation, but the rest of the output appears to be non-standard/ non-sensical- there is only one box in the simulation and the negative number as a molecule type seems odd.
>> 
>> 
>> Indeed the error messages do mean there is a problem.  When you perform a volume move in Towhee it scales the center of mass position of all the molecules (in a manner appropriate for the volume change) and then keeps all of the intramolecular distances the same.  This is not possible when the "molecule" spans the periodic images with its bonding pattern.
>> 
>> You would need a completely different move that scaled the intramolecular distances for the volume change.  That would then lead to problems with any molecule that has a rigid bond length (as the attempt to change that bond length would result in an infinite energy) and also would be fairly inefficient as the intramolecular distances are quite sensitive.
>>  
>> The volnpt.f file description from the towhee code manual notes that “you cannot use this move with a molecule that is bonded through the periodic boundary condition (like a zeolite).”  I suspect that the bonds in the montmorillonite molecules are across the periodic boundary and trigger the VOLNPT output message. However, this same note is listed for the volnvt.f file and there are no warnings generated.  Are these simulation results corrupt?  Is there a way to salvage this simulation or work around this problem?  The forcefield for the interactions is CLAYFF.  So, the bonds, angles, torsions, and improper  in the montmorillonite layers are zero energy.  I had to define these terms so that each montmorillonite layer can be a molecule that can move/ translate during the simulation.  Is there an alternate way to conduct this simulation and avoid the VOLNPT violation?
>> 
>> Only if every atom in the montmorillonite was a separate molecule.  However, be aware you are then changing the density of your montmorillonite and it is quite likely that is not what you are intending to sample.
>> 
>> I'm not sure if you were intending to sample the layer separation distance, but in that case you would need a new implementation of the volume move that only scale the volume in one of the dimensions instead of uniformly.
>> 
>> Marcus
>> 
>> -- 
>> Marcus G. Martin
>> 88 Martinez Road
>> Edgewood NM 87015-8222
>> land (505) 286 4457
>> cell (505) 363 3179
>> www.photobirder.com
>> towhee.sourceforge.net
>> 
> 
> Aric Newton
> 
> Laboratory of Nuclear and Environmental Materials
> Faculty of Engineering
> Hokkaido University
> Sapporo, Japan
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
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Aric Newton

Laboratory of Nuclear and Environmental Materials
Faculty of Engineering
Hokkaido University
Sapporo, Japan

Re: [Towhee-users] VOLNPT output: an error message?

[Aric N. <agn...@en...>]

Dear Marcus,

Thank you for your reply.  I understand that the errant output is a result of the model violating the constraints of the pmcell move by having bonds in each montmorillonite layer that cross the boundary.  The harmonic bonds that cross the boundary have spring constants of zero.  Thus, the energy of these bonds is independent of the positions of the atoms (i.e. it’s always zero).  This condition is a result of the parameters in the CLAYFF forcefield.  I have only “created” these bonds because I would like each montmorillonite layer to be able to translate (as a unit)  in the x-, y-, or z-direction as part of the MC moves.

I can create an input file without these zero-force constant “bonds”, in which case each atom in the montmorillonite is a molecule, but I have been unable to group these individual molecules into a super-molecule that I can then translate as a unit.  My starting simulation cell size is the equilibrium cell size from a 1.0 ns MD-NPT in LAMMPS, so I am not too worried about the changes in the MMT density.  With an anisotropic MC-NPT that only has a five percent probability of performing a pmcell move, I suspect that density fluctuations in the montmorillonite should be limited and, I am assuming, negligible.  Is this a reasonable assumption?

These simulations are part of a thermodynamic integration.  The model has only one box and the equilibrium cell parameters from the MD-NPT simulation confirm that my layer spacing and water content are consistent with the experimental condition that I am trying to simulate.  So, if the pmcell move adjusts the center of mass of each atom in the montmorillonite sheets in a manner appropriate with the volume change (adjusting interatomic distances), then that is what I want.  However, is there a way to also get the center of mass of each sheet to translate as part of the pmtracm command when in fact each sheet is composed of many molecules?  The pmplane move sounds close to what I want, but I am unsure how to define a dynamic definition of the plane so that it always includes only a montmorillonite sheet regardless of previous translation moves during the simulation. Do you have any suggestions or is simulating with rigid montmorillonite layers the only option with the current move algorithms?

Thank you,

Aric Newton


On Oct 6, 2014, at 10:02 AM, Marcus Martin <me...@gm...> wrote:

> On Fri, Oct 3, 2014 at 4:22 AM, Aric Newton <agn...@en...> wrote:
> 
> I am using towhee for a one box MC-NPT simulation of two montmorillonite layers with an interlayer space containing the counter ions and water molecules.  Each montmorillonite layer is treated as an individual molecule and moves as a unit via the pmtracm move probability.  I have previously equilibrated the system at high temperature in the NVT ensemble without any errors, but the output that I am getting now that I have switched to the NPT ensemble leaves me a bit uncertain.  In the towhee_output file, there are about 10,000 lines that read as below.   
> 
>  VOLNPT: move attemped in box that has a periodic bonded molecule
>  Molecule type:      -31414
>  Chain number:           1
>  Box:           2
> ...
> 
> The *.pdb snapshots are being output during the simulation, but the rest of the output appears to be non-standard/ non-sensical- there is only one box in the simulation and the negative number as a molecule type seems odd.
> 
> 
> Indeed the error messages do mean there is a problem.  When you perform a volume move in Towhee it scales the center of mass position of all the molecules (in a manner appropriate for the volume change) and then keeps all of the intramolecular distances the same.  This is not possible when the "molecule" spans the periodic images with its bonding pattern.
> 
> You would need a completely different move that scaled the intramolecular distances for the volume change.  That would then lead to problems with any molecule that has a rigid bond length (as the attempt to change that bond length would result in an infinite energy) and also would be fairly inefficient as the intramolecular distances are quite sensitive.
>  
> The volnpt.f file description from the towhee code manual notes that “you cannot use this move with a molecule that is bonded through the periodic boundary condition (like a zeolite).”  I suspect that the bonds in the montmorillonite molecules are across the periodic boundary and trigger the VOLNPT output message. However, this same note is listed for the volnvt.f file and there are no warnings generated.  Are these simulation results corrupt?  Is there a way to salvage this simulation or work around this problem?  The forcefield for the interactions is CLAYFF.  So, the bonds, angles, torsions, and improper  in the montmorillonite layers are zero energy.  I had to define these terms so that each montmorillonite layer can be a molecule that can move/ translate during the simulation.  Is there an alternate way to conduct this simulation and avoid the VOLNPT violation?
> 
> Only if every atom in the montmorillonite was a separate molecule.  However, be aware you are then changing the density of your montmorillonite and it is quite likely that is not what you are intending to sample.
> 
> I'm not sure if you were intending to sample the layer separation distance, but in that case you would need a new implementation of the volume move that only scale the volume in one of the dimensions instead of uniformly.
> 
> Marcus
> 
> -- 
> Marcus G. Martin
> 88 Martinez Road
> Edgewood NM 87015-8222
> land (505) 286 4457
> cell (505) 363 3179
> www.photobirder.com
> towhee.sourceforge.net
> 

Aric Newton

Laboratory of Nuclear and Environmental Materials
Faculty of Engineering
Hokkaido University
Sapporo, Japan

Re: [Towhee-users] VOLNPT output: an error message?

[Marcus M. <me...@gm...>]

On Fri, Oct 3, 2014 at 4:22 AM, Aric Newton <agn...@en...>
wrote:

I am using towhee for a one box MC-NPT simulation of two montmorillonite
> layers with an interlayer space containing the counter ions and water
> molecules.  Each montmorillonite layer is treated as an individual molecule
> and moves as a unit via the *pmtracm* move probability.  I have
> previously equilibrated the system at high temperature in the NVT ensemble
> without any errors, but the output that I am getting now that I have
> switched to the NPT ensemble leaves me a bit uncertain.  In the
> *towhee_output* file, there are about 10,000 lines that read as below.
>
> * VOLNPT: move attemped in box that has a periodic bonded molecule*
> * Molecule type:      -31414*
> * Chain number:           1*
> * Box:           2*
> ...
>
> The *.pdb snapshots are being output during the simulation, but the rest
> of the output appears to be non-standard/ non-sensical- there is only one
> box in the simulation and the negative number as a molecule type seems odd.
>
>
Indeed the error messages do mean there is a problem.  When you perform a
volume move in Towhee it scales the center of mass position of all the
molecules (in a manner appropriate for the volume change) and then keeps
all of the intramolecular distances the same.  This is not possible when
the "molecule" spans the periodic images with its bonding pattern.

You would need a completely different move that scaled the intramolecular
distances for the volume change.  That would then lead to problems with any
molecule that has a rigid bond length (as the attempt to change that bond
length would result in an infinite energy) and also would be fairly
inefficient as the intramolecular distances are quite sensitive.


> The *volnpt.f* file description from the towhee code manual notes that
> “you cannot use this move with a molecule that is bonded through the
> periodic boundary condition (like a zeolite).”  I suspect that the bonds in
> the montmorillonite molecules are across the periodic boundary and trigger
> the VOLNPT output message. However, this same note is listed for the
> *volnvt.f* file and there are no warnings generated.  Are these
> simulation results corrupt?  Is there a way to salvage this simulation or
> work around this problem?  The forcefield for the interactions is CLAYFF.
> So, the bonds, angles, torsions, and improper  in the montmorillonite
> layers are zero energy.  I had to define these terms so that each
> montmorillonite layer can be a molecule that can move/ translate during the
> simulation.  Is there an alternate way to conduct this simulation and avoid
> the VOLNPT violation?
>

Only if every atom in the montmorillonite was a separate molecule.
However, be aware you are then changing the density of your montmorillonite
and it is quite likely that is not what you are intending to sample.

I'm not sure if you were intending to sample the layer separation distance,
but in that case you would need a new implementation of the volume move
that only scale the volume in one of the dimensions instead of uniformly.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com
towhee.sourceforge.net

[Towhee-users] VOLNPT output: an error message?

[Aric N. <agn...@en...>]

Dear Towhee users and developers,

I am using towhee for a one box MC-NPT simulation of two montmorillonite layers with an interlayer space containing the counter ions and water molecules.  Each montmorillonite layer is treated as an individual molecule and moves as a unit via the pmtracm move probability.  I have previously equilibrated the system at high temperature in the NVT ensemble without any errors, but the output that I am getting now that I have switched to the NPT ensemble leaves me a bit uncertain.  In the towhee_output file, there are about 10,000 lines that read as below.   

...
  +++++ start of markov chain +++++

Move       Box   Energy [K]  Volume [A^3] Press. [kPa] Molecules
 VOLNPT: move attemped in box that has a periodic bonded molecule
 Molecule type:       19753
 Chain number:           1
 Box:           2
 VOLNPT: move attemped in box that has a periodic bonded molecule
 Molecule type:        4498
 Chain number:           1
 Box:           2
 VOLNPT: move attemped in box that has a periodic bonded molecule
 Molecule type:      -31414
 Chain number:           1
 Box:           2
...

The *.pdb snapshots are being output during the simulation, but the rest of the output appears to be non-standard/ non-sensical- there is only one box in the simulation and the negative number as a molecule type seems odd.

The volnpt.f file description from the towhee code manual notes that “you cannot use this move with a molecule that is bonded through the periodic boundary condition (like a zeolite).”  I suspect that the bonds in the montmorillonite molecules are across the periodic boundary and trigger the VOLNPT output message. However, this same note is listed for the volnvt.f file and there are no warnings generated.  Are these simulation results corrupt?  Is there a way to salvage this simulation or work around this problem?  The forcefield for the interactions is CLAYFF.  So, the bonds, angles, torsions, and improper  in the montmorillonite layers are zero energy.  I had to define these terms so that each montmorillonite layer can be a molecule that can move/ translate during the simulation.  Is there an alternate way to conduct this simulation and avoid the VOLNPT violation?

Thank you,

Aric Newton

[Towhee-users] cmix_pair_list (Thermodynamic Integration)

[Javad N. <nor...@ym...>]

 Dear All,

I am trying to perturb a single solute molecule in a solvent using TI method implemented in Towhee,
However, i have two atom with same name belonging to different molecules. How should i distinguish between them via cmix_pair_list parameter?

Bests,
JAVAD

[Towhee-users] Version 7.1.0

[Marcus M. <mar...@us...>]

Howdy Towhee users,

Version 7.1.0 is now available.  There were numerous small changes and bug
fixes as detailed in the release notes.

http://towhee.sourceforge.net/input/towhee_input_v7_1_x.html

One larger thematic change is that I am rebuilding the CBMC routines to
make them more general, and also more robust.  If things were already
working for you, then you should see absolutely no change in your results
with the current version (although there is always hope it is a bit faster
now with some of the logic consolidation, but still the majority of
simulation time is spent computing energy terms anyways).  If you were
previously experiencing a problem on a molecule that resulted in a code
failure for any combination of the CBMC terms please try that out with the
new version and if it is still not working then I would welcome submissions
(directly to my email) of input files that result in those problems.

thanks,

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com
towhee.sourceforge.net

Re: [Towhee-users] non standard forcefields

[André F. de M. <afd...@gm...>]

Dear Marcus,

Thank you for the suggestions!

I have been trying these options I sketched in my previous message and thus
far I've been able to run a few simulations without any bonding for the
rigid nanoparticle, using a copy of the OPLS-aa FF as a starting point,
just as you suggested, but this is not totally satisfactory. I'll try your
suggestions and as soon as I get them working we'll be back on the
"parallel Towhee discussion", I'm certainly interested in that.

cheers,

Andre



On Fri, Jul 11, 2014 at 1:11 PM, Marcus Martin <me...@gm...> wrote:

> On Wed, Mar 19, 2014 at 5:26 PM, André Farias de Moura <
> afd...@gm...> wrote:
>
>
>> I'm planning to study the solvation patterns of a capped nanoparticle,
>> which has a ceramic core surrounded by organic molecules (chemically
>> attached to the ceramic core). The point is that the core is hardly
>> accessible to the solvent and the organic layer might be conveniently
>> treated by any regular forcefield (OPLS for instance) and I expect that
>> this organic layer should play the only relevant role in the interactions
>> with the solvent, the ceramic core being just an excluded volume and
>> shape-defining element of my model.
>>
>> Here comes the issue I'm facing: any standard forcefield which is
>> adequate for the organic part lacks parameters for the ceramic part (Cd and
>> inorganic S atoms). I tried to manually edit the towhee_ff_OPLS-aa file to
>> add Cd atoms (not the Cd2+ ion), replacing one of the carbon atom types
>> available there, but then I got a huge number of errors while trying to run
>> towhee, mostly related with missing bonding terms (vibrations, angles and
>> dihedrals).
>>
>> One option that apparently worked but I guess it will become a trouble
>> quite soon is to set the number of vibrations to zero for all atoms
>> comprising the capped nanoparticle in the towhee_input file, which seems to
>> work as long as I keep the whole structure still, no MC movement
>> whatsoever. It works for a single nanoparticle, but eventually I'll be
>> interested in the interactions between nanoparticles, and then this
>> approach will become inadequate. It seems to me that it wouldn't work
>> either using the NPT ensemble, am I right?
>>
>
> Setting the number of vibrations to zero is an extreme choice.  This is
> allowed, but is intended for use with porous solids where you are not
> interested in moving that "molecule" or sampling its conformation.  I do
> not think this applies to your case where you want a rigid interior with a
> flexible exterior.
>
>
>> Assuming that a fully rigid structure suffices all my needs for the time
>> being, should I try to write down a customized forcefield with all types of
>> bonding interactions as dummy interactions (either setting all of them to
>> "no interaction" or setting the force/energy constants to zero). Would it
>> be enough to make towhee understand that atoms are bonded and should be
>> moved as a rigid body?
>>
>
> If you want the atoms to be bonded and moved as a rigid body then the best
> approach is to have your custom forcefield use all of the rigid options for
> bond lengths, angles, and dihedrals.
>
> I would also suggest that it is a good practice when extending an existing
> forcefield to not overwrite the original files with your new parameters,
> but instead to create a second file that contains your additions.  An
> example of how I have done this is provided in the Charmm27x file
>
> http://towhee.sourceforge.net/forcefields/charmm27x.html
>
> Making your changes in this manner has the dual benefit of not having your
> changes accidentally overwritten when you use a new version of Towhee, and
> also making it abundantly clear when you write your paper which parameters
> are your additions and which are the originals.
>
>
>> I did something like that to make towhee accept slightly distorted TIP3P
>> water molecules from a previous molecular dynamics simulation and it
>> worked, but I would like to have some advices on maybe some alternative
>> approach because the capped nanoparticles are quite large, at least 335
>> atoms.
>>
>> Any suggestions and comments will be really appreciated!
>>
>
> That is a big and complicated molecule that is probably right on the edge
> of what is currently possible with CBMC.  If it does contain the rigid core
> you mentioned above then you will want to consider setting the nmaxcbmc
> value to something that is the size of the flexible outer chains on the
> molecule so that the CBMC move is only trying to regrow some of the outer
> chains instead of the entire molecule.
>
> A system with a single solvated nanoparticle is already fairly large, and
> as soon as you want to study more than one nanoparticle that will lead to
> us having the "parallel Towhee discussion".
>
> Marcus
>
> --
> Marcus G. Martin
> 88 Martinez Road
> Edgewood NM 87015-8222
> land (505) 286 4457
> cell (505) 363 3179
> www.photobirder.com
>



-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

Re: [Towhee-users] VLE

[Marcus M. <me...@gm...>]

On Wed, Mar 5, 2014 at 12:33 AM, <roh...@ge...> wrote:


> I have a technical question about Towhee capabilities and I appreciate if
> anybody can give me an answer.
> Is it possible to simulate Water droplet condensation on a steel surface
> when  steel is in contact with a
> supercritical fluid with dissolved water?
> In other word, let's say we have SO2+tiny amount of water in supercritical
> state, from thermodynamic I know
> that this system is single phase and I do not expect water as a separate
> phase. What if this system be in contact
> with a solid phase like steel?
>

As I continue working through the Towhee emails I find I get this sort of
email quite a bit and I want to address it in a general way in the hope
this answers future similar questions as well.

People often ask me "Can I simulate this particular system?" and I feel
like they are asking the wrong question.

At this point you can set up just about any complex system in Towhee and
"simulate it" by running a simulation with one of the forcefields already
in the code.

Therefore I can "simulate" HIV-protease because I can set up that system,
add in waters, and successfully run Towhee in order to produce output.  Why
the literature is even packed with lots of people who have "simulated"
HIV-protease using a wide variety of molecular simulation packages.
 Clearly HIV-protease is within the realm of "things that can be simulated".

The goal of molecular simulation is not just "to simulate", but to make
predictions that have a reasonable accuracy when compared with theory or
experiment.  So if the question you ask instead is "Can I start with a
random conformation of HIV-protease in water and use Towhee to predict the
crystal structure within 3 Angstrom root mean square error?" I would say,
probably not with current methods but if you figured out how you would
likely win a Nobel prize.  If the question was "Can I start with the
crystal structure of HIV-protease, solvate it with a water model, and then
predict the binding constant of a particular drug candidate within an order
of magnitude of experiment?" then I would say that is right at the edge of
what is possible with the most determined set of research codes and expert
users and while I am not sure if we can do that yet, I would love to be
part of a multi-person effort to advance the force fields and algorithms
with that goal in mind.

So for anyone who is wondering about a particular property they wish to
predict for a particular system in the future my best advice is for them to
consult the literature to see what has already been done on similar systems
and use that as a rough guide for what sorts of accuracy might be expected
for the quantities they desire to predict via molecular simulation.  If you
cannot find any similar successful simulations in the literature then you
should prepare for a year of work to develop and/or test your potentials
against known experimental results before moving into the world of making
useful predictions.

In the particular case of Silicon dioxide, water, and a steel surface asked
about in this email I suspect your literature search will show that mixing
metal and organic forcefields is challenging but hopefully you can find
some folks who have done something similar to give you a starting place in
your efforts.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Re: [Towhee-users] non standard forcefields

[Marcus M. <me...@gm...>]

On Wed, Mar 19, 2014 at 5:26 PM, André Farias de Moura <afd...@gm...>
wrote:


> I'm planning to study the solvation patterns of a capped nanoparticle,
> which has a ceramic core surrounded by organic molecules (chemically
> attached to the ceramic core). The point is that the core is hardly
> accessible to the solvent and the organic layer might be conveniently
> treated by any regular forcefield (OPLS for instance) and I expect that
> this organic layer should play the only relevant role in the interactions
> with the solvent, the ceramic core being just an excluded volume and
> shape-defining element of my model.
>
> Here comes the issue I'm facing: any standard forcefield which is adequate
> for the organic part lacks parameters for the ceramic part (Cd and
> inorganic S atoms). I tried to manually edit the towhee_ff_OPLS-aa file to
> add Cd atoms (not the Cd2+ ion), replacing one of the carbon atom types
> available there, but then I got a huge number of errors while trying to run
> towhee, mostly related with missing bonding terms (vibrations, angles and
> dihedrals).
>
> One option that apparently worked but I guess it will become a trouble
> quite soon is to set the number of vibrations to zero for all atoms
> comprising the capped nanoparticle in the towhee_input file, which seems to
> work as long as I keep the whole structure still, no MC movement
> whatsoever. It works for a single nanoparticle, but eventually I'll be
> interested in the interactions between nanoparticles, and then this
> approach will become inadequate. It seems to me that it wouldn't work
> either using the NPT ensemble, am I right?
>

Setting the number of vibrations to zero is an extreme choice.  This is
allowed, but is intended for use with porous solids where you are not
interested in moving that "molecule" or sampling its conformation.  I do
not think this applies to your case where you want a rigid interior with a
flexible exterior.


> Assuming that a fully rigid structure suffices all my needs for the time
> being, should I try to write down a customized forcefield with all types of
> bonding interactions as dummy interactions (either setting all of them to
> "no interaction" or setting the force/energy constants to zero). Would it
> be enough to make towhee understand that atoms are bonded and should be
> moved as a rigid body?
>

If you want the atoms to be bonded and moved as a rigid body then the best
approach is to have your custom forcefield use all of the rigid options for
bond lengths, angles, and dihedrals.

I would also suggest that it is a good practice when extending an existing
forcefield to not overwrite the original files with your new parameters,
but instead to create a second file that contains your additions.  An
example of how I have done this is provided in the Charmm27x file

http://towhee.sourceforge.net/forcefields/charmm27x.html

Making your changes in this manner has the dual benefit of not having your
changes accidentally overwritten when you use a new version of Towhee, and
also making it abundantly clear when you write your paper which parameters
are your additions and which are the originals.


> I did something like that to make towhee accept slightly distorted TIP3P
> water molecules from a previous molecular dynamics simulation and it
> worked, but I would like to have some advices on maybe some alternative
> approach because the capped nanoparticles are quite large, at least 335
> atoms.
>
> Any suggestions and comments will be really appreciated!
>

That is a big and complicated molecule that is probably right on the edge
of what is currently possible with CBMC.  If it does contain the rigid core
you mentioned above then you will want to consider setting the nmaxcbmc
value to something that is the size of the flexible outer chains on the
molecule so that the CBMC move is only trying to regrow some of the outer
chains instead of the entire molecule.

A system with a single solvated nanoparticle is already fairly large, and
as soon as you want to study more than one nanoparticle that will lead to
us having the "parallel Towhee discussion".

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Re: [Towhee-users] (no subject)

[Marcus M. <me...@gm...>]

On Mon, Apr 21, 2014 at 12:37 PM, Meysam Makaremi <mey...@gm...
> wrote:


> I'm trying to do some NPT simulations for different water molecules to
> measure the chemical potential. Towhee works fine for SPC water molecules
> but when I'm trying TIP4P water molecules and using towhee_ff_TIP4P, after
> some steps, I get this error:
>
>  GETCBANGLE: all choices have infinite energy
>  for the angle B selection
>  molecule type:           1
>  iufrom,iuprev,ntogrow:           1           2           2
>
>  I checked the maillist for this problem and found some other people have
> the same issues:
> http://sourceforge.net/p/towhee/discussion/298240/thread/2a3932a4/#e64e
>

Continuing to work my way through the backlog of Towhee emails.

Sounds like a recurring issue that is probably related to all of the rigid
bond and angle terms in that molecule making CBMC difficult.

If anyone has input files that reproduce this problem (hopefully in a
relatively few number of cycles) I would appreciate them sending them to me
so I can track down what is going wrong.

thanks,

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Re: [Towhee-users] Decompose individual chemical potentials

[Marcus M. <me...@gm...>]

On Mon, May 5, 2014 at 7:41 AM, Mohan maruthi sena <mar...@gm...>
wrote:


>             I have performed a MC simulation using towhee on a mixture of
> water+methane for 1000 MC moves and  I want to calculate chemical potential
> of water from the mixture. I got the following output,
>

A comment: 1000 Monte Carlo moves is an extremely short simulation for
computing something that is as notoriously difficult as the chemical
potential of liquid water.

 u (Density)               K    1    -3724.211
>  u (NVT Insertion)         K    1    -1631.175
>  u (NpT Insertion)         K    1    -1632.062
>  u (Den. + NVT Insert)     K    1    -5355.386
>  u (Den. + NpT Insert)     K    1    -5356.273
>  u (Gibbs Total)           K    1    -5352.923
>  u (Density)               K    2    -3013.721
>  u (NVT Insertion)         K    2      146.384
>  u (NpT Insertion)         K    2      146.339
>  u (Den. + NVT Insert)     K    2    -2867.337
>  u (Den. + NpT Insert)     K    2    -2867.382
>  u (Gibbs Total)           K    2    -2866.887
>

My question is, How can i find the chemical potential of water from the
> output?
>

The above snippet contains all of the various ways chemical potential is
computed in Towhee.  For more discussion about what each of those mean
please see the manual section about the chemical potential.

http://towhee.sourceforge.net/algorithm/chemicalpotential.html

The short answer is: use the Gibbs Total value for the molecule type you
are interested in measuring.  Again, you will want a much longer simulation
to get a reliable and useful answer.  You can then convert from the
statistical mechanics shorthand of K/k_B to your favorite energy unit by
multiplying by the appropriate form of Boltzmann's constant.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

[Towhee-users] Version 7.0.7 released

[Marcus M. <mar...@us...>]

Howdy Towhee users,

Version 7.0.7 of Towhee is now available.  This is mostly a maintenance
release with minor changes to address some compiler warnings on
OSX-Mavericks.  It also has updates to the manual including a new suggested
Towhee reference of the review article I published about Towhee last year
in Molecular Simulation.

M. G. Martin; "MCCCS Towhee: a tool for Monte Carlo molecular simulation",
Mol. Simulat. 39 1212-1222 (2013).

Ideally, most users would read this paper in addition to citing it when
using Towhee, but I want to especially bring section 4 of that paper to the
attention of any relatively new users who are performing vapor-liquid
coexistence simulations in Towhee.  My hope is reading that section will
get most folks well on their way to successfully and efficiently performing
vapor-liquid coexistence simulations.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com