MCCCS Towhee Activity
Brought to you by:
marcus_martin
Activity for MCCCS Towhee
-
long xu posted a comment on discussion Help
Hello, Marcus. I uploaded the relevant literature as an attachment, the appendix of the article shows the author's source program, but I don't know why I can't run it, and some keywords in the source code such as lperiod_xyz; wall_thick; n_hole; hole_dimen; wall_type, I have not seen the explanation on the website of the software, I hope you can help me to answer it. Thanks.
-
Marcus Martin posted a comment on discussion Help
Do you have a copy of that paper or at least a reference for me to look at? I am not familiar with those terms, but I am a bit out of the loop on the literature these days. Marcus
-
After reading relevant literature, I found that some people put forward two methods, Gauge-gemc and Gauge-gcmc. I would like to ask someone who knows this method, does this method need to modify the underlying program of towhee, or is the operation mode different, or how to achieve it?
-
Hello towhee users, I am a new user and would like to ask what the normal simulation process of towhee is like, For example, I want to use NVT ensemble to simulate the pressure and density of C3H8 molecules at a certain temperature. Should I first create a pdb file filled with C3H8 molecules, then convert it into the coods file required by towhee software with pdb2towhee, and then find similar input files in the sample example? Modify related parameters. After the simulation is over, what files should...
-
Dzmitry Hlushkou posted a comment on discussion Open Discussion
Hallo everybody, Could someone kindly help me to estimate the speed of the simulations. In my case, the simulation with the attached input-file takes about 60 minutes (NpT ensemble, 1000 cycles for 645 water molecules at the standard conditions in a 3 nm x 3 nm x 3 nm box). I would be extremely grateful if someone could repeat this simulation and let me know the time and CPU used. Thank you a lot in advance. PS. Of course, the path to my Force Field directory must be change to yours.
-
Xu Yan modified a comment on discussion Open Discussion
Hello, Marcus Thank you for your response. I have already attached the input and output files below. Could you please take a look at why the volume of the third box is changing? Additionally, I plan to change the periodic boundary conditions for the x and y directions of the third box. In which file should I make these modifications? Thanks a lot. Xu
-
Hello, Marcus Thank you for your response. I have already attached the input and output files below. Could you please take a look at why the volume of the third box is changing? Additionally, I plan to change the periodic boundary conditions for the x and y directions of the third box. In which file should I make these modifications? Thanks a lot. Xu
-
Hello, Marcus Thank you for your response. I have already attached the input and output files below. Could you please take a look at why the volume of the third box is changing? Additionally, I plan to change the periodic boundary conditions for the x and y directions of the third box. In which file should I make these modifications? Thanks a lot. Xu
-
Looking at the pdb files can be deceiving as you have some molecules wrapping periodically through the box so that can make it look like the molecules are outside of the box, when really they are wrapping around to the other side of the box (each molecule has its center of mass in the box, but the atoms may stick out). That picture of the system after 20000 moves does look strange. If you include all the input and output files from the run I have a much better chance of figuring out what is going...
-
Looking at the pdb files can be deceiving as you have some molecules wrapping periodically through the box so that can make it look like the molecules are outside of the box, when really they are wrapping around to the other side of the box (each molecule has its center of mass in the box, but the atoms may stick out). That picture of the system after 20000 moves does look strange. If you include all the input and output files from the run I have a much better chance of figuring out what is going...
-
Hello, Marcus Martin May I ask you a question about the gauge-NPT-GEMC. I am working on the oil mixture (C1 to C7) phase behavior with confined condition. I have three boxes, and the third box contains a carbon nanotube. The third box have to keep the volume being constant working as a gauge meter, hence, I set pmvlpr parameter like "0.5d0, 1.0d0, 0.0d0". The output on the terminal shows that the third box volume can be cosntant. But, question is that when I check the pdb file on the OVITO, the third...
-
XiaoZhan posted a comment on discussion Help
Hello,Marcus, I had the same problem, when I run the GCMC simulation, the output pdb file is not the same as the box of the settings, can you please solve this problem？ I use towhee_coords to generate my initial coordinates, but due to periodicity, the output of the PDB file is not as good as in the towhee_coords I set.
-
Done.
-
make towhee cc towhee.c -o towhee towhee.c: In function ‘print_usage’: towhee.c:337:18: error: ‘PACKAGE_VERSION’ undeclared (first use in this function) 337 | char version[] = PACKAGE_VERSION; | ^~~~~~~~~~~~~~~ towhee.c:337:18: note: each undeclared identifier is reported only once for each function it appears in make: *** [<builtin>: towhee]</builtin> Error 1
-
Dear Sir, i have install the GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 but there is error, how to solve this problem? make towhee DPACKAGE_NAME=\"towhee\" -DPACKAGE_TARNAME=\"towhee\" -DPACKAGE_VERSION=\"6.2.7\" -DPACKAGE_STRING=\"towhee-6.2.7\" -DPACKAGE_BUGREPORT=\"towhee-bugs@lists.sourceforge.net\" -DPACKAGE=\"towhee\" -DVERSION=\"6.2.7\" -DHAVE_STRSTR=1 -I. -c -o accumulateaverages.o accumulateaverages.F /bin/bash: line 1: -DPACKAGE_TARNAME="towhee": command not found make: [Makefile:658:...
-
wangqianqian modified a comment on discussion Open Discussion
Hello everyone, I am currently working on calculating the potential of mean force between two particles. Initially, I obtained the radial distribution function and utilized the program rdf2pmfpair to convert it into a potential of mean force. However, I suspect there might be issues with the radial distribution function, leading me to two specific questions: I'm curious to know if Towhee supports the implementation of umbrella sampling. If it does, could you please provide some guidance on how to...
-
Hello everyone, I am currently working on calculating the potential of mean force between two particles. Initially, I obtained the radial distribution function and utilized the program rdf2pmfpair to convert it into a potential of mean force. However, I suspect there might be issues with the radial distribution function, leading me to two specific questions: I'm curious to know if Towhee supports the implementation of umbrella sampling. If it does, could you please provide some guidance on how to...
-
There is not currently an option for cylindrical unit cells. That isn't a shape that can be periodically repeated to fill space so I am not sure how that would work. If you have a reference to something that describes how that unit cell would function I can take a look at it and estimate how much work it would be to implement.
-
In my point, maybe cylindrical cell can not be set in the towhee.
-
Hello, I encountered the same problem, how did you solve it?
-
Jessie posted a comment on discussion Open Discussion
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="Generator" content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:DengXian; panose-1:2 1 6 0 3 1 1 1 1 1;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} @font-face {font-family:"\@DengXian"; panose-1:2 1 6 0 3 1 1 1 1 1;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal...
-
Hello Marcus and everyone, I read a towhee input file from a dissertation (screenshot is attached). It seems to control the boundary conditions. However, I cannot find the command on the input file 8.2.x versions manual and on the previous version. I was wondering if anyone knows the meaning of this two lines and how to turn off the periodic boundary condition in the z direction. Any advice would be greatly appreciated. Best regards, Jessie
-
Hello everyone, I'm trying to run nitrogen adsorption in a cylindrical crystalline silica pore via GCMC. I first ran it in a simulation box with 63 angstrom length as the case in the bulk phase to get the relationship between the chemical potential and the vapor density in GCMC. Then I ran it in a cylindrical crystalline silica pore with D=40 angstrom. However, nitrogen filled full of the pore when the pressure (use the density in the bulk GCMC simulation and NIST database) is corresponding to 0.1...
-
Hi Marcus, Sorry that I did not get back to you sooner. I found the x,y and z are fluctuating from the .pdb files. I was trying to send to you .pdb files, but the system is blocked my reply several times. Therefore, I attached several screenshots from Ovito. Best regards, Jessie
-
Howdy Jessie, Looks like a constant volume cube of 63 by 63 by 63. What evidence do you have of the x, y, and z values fluctuating? Marcus Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 (505) 363 3179 www.photobirder.com towhee.sourceforge.net
-
Hi Marcus, Thank you so much for your quick reply. Sure, I attached the output file. Best, Jessie
-
Howdy Jessie, I do not see anything that would be changing the box size, especially given this is a grand canonical simulation. Can you include the output from that simulation so I can check to see that the box values are really changing and not just something else related to x,y,z (like maximum translation values)? Marcus On Wednesday, March 22, 2023, Jessie jessie20230322@users.sourceforge.net wrote: Hello everyone, I'm trying to use GCMC to simulate the nitrogen behavior in the bulk phase at 77.4k....
-
Hello everyone, I'm trying to use GCMC to simulate the nitrogen behavior in the bulk phase at 77.4k. I thought the box size should be fixed during the simulation like what I got from LAMMPS. However, the x, y, z of the box fluctuating all the time, although the volume is the same as what I set from the output file. Could you please help to check the code? I attached the whole input file. Thank you so much! Best regards, Jessie input: ensemble 'uvt' temperature 77.4d0 nmolty 1 nmolectyp 100000 chempot...
-
Raj Akshat posted a comment on discussion Help
Hi, While installing towhee, I received an error 127 while giving a command make towhee. Could you please help me with resolving the error? Thank you.
-
Hi, I saw the following description from the towhee website, "As an alternative to either manually modifying the ForceFields files or creating symbolic links, execute the relocate_examples.pl script in the Examples directory. This script copies all the examples to a directory named test in the towhee root directory, and will simultaneously rewrite all references to /towheebase appropriately. You can then execute examples in the normal fashion from the test directory." I donnot find the relocate_examples.pl...
-
Anson Thomas posted a comment on discussion Open Discussion
Dear experts, I am trying to find out the number of molecules that must be added water molecules to my simulation box (of goethite, an oxide of iron) as done in the following papers (https://doi.org/10.1088/1361-648x/aa7e4f and https://doi.org/10.1088/0953-8984/24/12/124105) Since I am totally new to the field, I started with the example "Grand_Canonical_Ensemble/Walt2001_Nanotube". I modified the input according to my system, and used towhee_coords file to give the coordinates. I wanted to use the...
-
Hello, I am honored to recive your patient reply. I made a mistake. I always thought the MPI version could not process multiple jobs, probable beacuse I have been computing the jobs on my own laptop. WangQianqian
-
Howdy, They are processed at the same time. If you run a list of 4 jobs on 4 nodes then it is 1 job per node until they are all done. Marcus On Tue, Aug 23, 2022 at 3:21 AM wangqianqian wqq@users.sourceforge.net wrote: Thanks very much! 1. So, I understand that the MPI version of Towhee which reads from an additional file (towhee_parallel) is not able to be processed by multiple processors, right? 2. In fact, the file(towhee_parallel ) is a batch file, when I use the option towhee -p jobfarm to process...
-
Thanks very much! 1. So, I understand that the MPI version of Towhee which reads from an additional file (towhee_parallel) is not able to be processed by multiple processors, right? 2. In fact, the file(towhee_parallel ) is a batch file, when I use the option towhee -p jobfarm to process the 4 task, this 4 task will not be processed at the same time, but processed one by one? Is there some different from the serial ? While, the parallel programe generally can be processed by multiple processors.
-
Pretty much the same, maybe a tiny amount more overhead. Using 4 processors to compute a single task is just 3 processors waiting around while the other one runs the simulation. Perhaps slightly slower due to how your machine communicates. Really want to have more (or equal) jobs than processors for jobfarming.
-
Hi, 1. using the towhee_parallel to calculate a single task, is it the same as calculating a task serially? 2. using the option mpirun -np 4 towhee -p jobfarm to calculate a single task, why the time is longer than using the option towhee -p jobfarm? Thank you very much!
-
using the towhee_parallel to calculate a single task, is it the same as calculating a task serially? using the option mpirun -np 4 towhee -p jobfarm to calculate a single task, why the time is longer than using the option towhee -p jobfarm?
-
Paul modified a comment on discussion Help
Hello there, I'm trying to carry out some MC simulations of cyclopentane with Towhee using the TraPPE potential. If I'm reading the manual correctly the torsion coefficents should be c0 = 0.5020000000E+03 c1 = 0.4591400000E+05 c2 = -0.1651800000E+05 c3 = 0.1496000000E+04 and the bend coefficient K = 0.3125000000E+05 Which are quite large and I'm having some trouble generating realistic conformations for this molecule. So far I've tried many different combinations of cbmc parameter values and generation...
-
Hello there, I'm trying to carry out some MC simulations of cyclopentane with Towhee using the TraPPE parameters. If I'm reading the manual correctly the torsion coefficents should be c0 = 0.5020000000E+03 c1 = 0.4591400000E+05 c2 = -0.1651800000E+05 c3 = 0.1496000000E+04 and the bend coefficient K = 0.3125000000E+05 Which are quite large and I'm having some trouble generating realistic conformations for this molecule. So far I've tried many different combinations of cmbc parameter values and generation...
-
Mukesh Kumar posted a comment on discussion Open Discussion
Hello My name is Mukesh I have been trying to simulate CO2 in silica(SiO2) slit pore as per the example in towhee. However, I was unable to understand the H-matrix and initial lattice concept particularly for slit pore. The output pdb file looks some thing like this image.png (attached) From the pdb file I could see the that most of the CO2 molecules are out of the slit pore . I acually want the whole CO2 molecules to be inside slit pore. Could you please help me in resolving this issue. Sincerely,...
-
Aparna Singh posted a comment on discussion Help
Dear Marcus, I want to use the TraPPE-EH force field for N2. In TraPPE-EH towhee file, how N2 parameters are used as per J. Potoff; J. I. Siepmann; "Vapor-Liquid Equilibria of Mixtures Containing Alkanes, Carbon Dioxide, and Nitrogen", AIChE J. 47 1676-1682 (2001). Is there any formula used for parameters in the file? Kindly please help me regarding the same. Awaiting your reply. Regards, Aparna
-
MCCCS Towhee released /towhee/towhee-8.2.3.tar.gz
-
version 8.2.3
-
-
version 8.2.2
-
I could not reproduce this error. That command worked for me on my development machine. Were you using the mpi compiled version of the code (enabled with the -enable-mpi configuration flag prior to compiling) when running this command? Strange that there is screen output in this portion as when using the MPI compiled version of Towhee that gets sent to a different file.
-
Bug addressed in version 8.2.2.
-
Bug fix for this issue addressed in version 8.2.2.
-
HAMMOURI Mostapha posted a comment on discussion Help
Dear Towhee-Mailing List, I would like to reproduce with the towhee software some vapor-liquid coexistence curve. As a starting point I took the towhee_input file that is in the examples of towhee (Canonical_Ensemble/wall_Water). I have successfully tested the execution of the towhee_input file, but when I change the temperature to see the variation in density, the latter remains constant even though I increased the number of steeps. However, I'm unable to reproduce the vapor-liquid curves as described...
-
Craig Fisher created ticket #17
gfortran 10 detects type-mismatch error
-
Manjul Yadav created ticket #16
MPI not supported
-
José Paulo Mota posted a comment on discussion Open Discussion
Dear Martin, It seems to me that the local variable 'thetatwo' in 'checkstruc.F' should be 'double precision' not 'integer'. Regards, Paulo
-
Tarik Ammouli posted a comment on discussion Open Discussion
I'm trying to simulate an adsorption isotherm of Dichlorobenzenes molecules using the NPT-ensemble with only 2 boxes (one for the adsorbent, & other for the reservoir). The problem that after couple of munîtes of running the simulation, the calculation stoppes because of this error : GETCBDIHED: problem finding old phidisp: -179.945919022886 ipeak,delta_dist: 1 179.994691340348. The MC moves that i've used for this simulation are : pmvol 0.125d0 pmvlpr 1.0d0 0.0d0 rmvol 0.1d0 tavol 0.5d0 pm2boxrbswap...
-
mohd rafie shaharudin posted a comment on discussion Help
Hi, I have a simulation system that combine molecular dynamics simulation with monte carlo in grand canonical ensemble. I have some issue when transferring coordinates from MD to MC as there are some deviation in bond length and angle that is above tolerance allowed inTowhee. To solve this issue, I compile my own towhee code and adjusted the tolerance of bond length (from source code value of 0.01 to 0.05) for bond style of fixed bond length. The same is done for angle but adjusted in the forcefield...
-
Hi, I run a simulation with 500K steps in GCMC to adsorb water into a graphene oxide membrane (GOM). The GOM are rigid and i only supply the chemical potential value of water. When i run one long simulation with 500K steps. i received this error; major problem in rosenbluth hard overlap in intermolecular The weird part is that this error does not appear when i break the simulation into few shorter simulation and take the final output file as the initial file to continue the simulation until i have...
-
Dear everyone, I want to calculate the free energy of mixture (for example water + ethanol). Which software can product coordinates of unit in the towhee_initial file. Thanks.
-
Hi, may i know if you have solved this issue? I'm having the same issue. This is the error message that i received: major problem in rosenbluth hard overlap in intermolecular Please let me know if you could get the system working. Thank you! Rafie
-
Even Nordhagen posted a comment on discussion Help
Now I'm able to initialize my system! But I still don't know what wrong with the approach above. Anyway, thank you for the help, this thread can be closed. Even
-
Many thanks for the prompt reply. As you say, the initial configuration is not important as one can always equilibrate the system to a more chaotic and realistic configuration. My problem is that I get overlapping configurations no matter what my initial configuration is (even if I start from an ordered lattice structure). Let's say I want to initialize a system to consist of 512 water molecules. As the initial configuration does not matter, this can be accomplished in several ways. The simplest...
-
Howdy Even, I put very little effort into constructing a starting configuration for my simulations since it should not matter much once the system starts running and sorts everything out. Unless you are setting up a molecule that will not move (like a porous solid) you can in theory start from anything and get to a good configuration by just doing some of the simple translation and rotation moves. You have encountered the one time when that does not work, namely when there is a hard overlap. While...
-
Hi, I would like to use Towhee to simulate water in the canonical ensemble. For the time being it doesn't matter which water model I use, so I started from the Wall_Water example which uses the SPC-E model. This example runs as expected, and I also managed to strip the towhee_initial file, rename it as towhee_coords and run the example again with initstyle='coords', as explained in the manual. However, I have a hard time figuring out how to initialize my own water system. What I want is to be able...
-
Hi, I would like to use Towhee to simulate water in the canonical ensemble. For the time being it doesn't matter which water model I use, so I started from the Wall_Water example which uses the SPC-E model. This example runs as expected, and I also managed to strip the towhee_initial file, rename it as towhee_coords and run the example again with initstyle='coords', as explained in the manual. However, I have a hard time figuring out how to initialize my own water system. What I want is to be able...
-
Kurt Lust posted a comment on ticket #15
Sorry for not answering sooner. The mail from SourceForge landed in my spam folder. I tested 8.2.1. There is one problem remaining: Source/schedule.F line 277 where the closing paranthese is in column 73. Since you are so responsive and take bug reports serious, I decided to invest some more time into it. I modified that file (split the line) and I can confirm that after that change it compiled on both a CentOS/RHEL 8 and CentOS/RHEL 7 system with the Intel 2020 compilers (using the original release...
-
Thanks for that bug report. Other people had similar issues lately so I had already been working on a fix. The configure file was modified to work better with Intel compilers and I also fixed that mistake where I went over the line limit with the preprocessor options. Version 8.2.1 is now available and should resolve your problems. If you see anything else please let me know. I do not have a machine setup with the combination of operating system and compiler that is giving folks trouble (seems like...
-
-
-
version 8.2.1
-
Code in violation of the Fortran standard for fixed format sources.
-
Hi Dr Marcus, Thank you for the explanation. Your suggestion is one of the options that I have tried but it is taking too much time for re-adsorption as i will have a system with hundreds of water molecules. This is the initial test I did for a simpler system. I would try to figure out a way with gromacs to ensure the angle is within the tolerance allowed in tip3p-ew forcefield. You have been really helpful and I am grateful now i understand what is going on with my simulation. Thank you so much...
-
Howdy Rafie, Did some debugging now that we have the files sorted out. Here are the angles computed for the 4 water molecules in your system (in degrees) imolty,units,angle,: 1 3 1 2 104.39856834930609 imolty,units,angle,: 1 3 1 2 104.46425669231122 imolty,units,angle,: 1 3 1 2 104.53565304465687 imolty,units,angle,: 1 3 1 2 104.29203343601303 That last one is outside of the tolerance allowed for the rigid angle by the default TIP3P-EW settings. To be honest, I was surprised that the other 3 were...
-
Hi, Im sorry for the mistake, here i attach the correct forcefield file for GO. Fo your information, the coordinate is taken from an MD simulation using Gromacs before I transfer the coordinate in Towhee to run further adsorption simulation. Thank you for your kind help. I really appreciate it! Regards, Rafie
-
The towhe_ff_GO file you provided appears to be a copy of the towhee_ff_TIP3P-EW file and so I get error messages related to not finding the parameters for the atomtype 'CA'. If you can try to provde the correct version of the towhee_ff_GO file I can take a look at the problem in more detail. From looking at your towhee_output file the error is happening for the first water molecule in your simulation. That is using a rigid angle so I assume the angle computed from the first 3 atoms must not be quite...
-
Hi Dr Marcus, Thank you for your reply. I have manage to figure out the errror which you adress as I have a different order of molecules in my coords file. I have updated my coords file as you suggest and manage to solve teh 'PUTARBINBOX' issue. However, i still could not get the simulation running with an error on overlap initial configuration as below; "ENGTOTAL: overlap bending imolty,ii,ip1,ip2 1 3 1 2 MAINLOOP: overlap in initial configuration" I'm a bit confused on how to track the error given....
-
Looks like you were also using your own forcefield files so I cannot run this without them. I did take a look at the towhee_output and have some comments that might help. The error means the first chain in the system, which is molecule type 1, has a problem for the bond between atom 2 and atom 1. That means the first water molecule in your simluation, and the bond between the oxygen and hydrogen. The bond length is computed as 1.35974262270475, and it is bond type 1 in the simulation. If I go back...
-
Hi, I have a code to transfer coordinate from gromacs to towhee. However when i run simulation in towhee, i have an error that says: Initial Energies for Box 1 overlap vibration chain,molecule,atom A,atom B 1 1 2 1 bond length: 1.35974262270475 bond type: 1 MAINLOOP: overlap in initial configuration I'm not sure how to detect which molecules are overlapping. Could anyone point out what is the problem with the set up? I will really appreciate that! My simulation is a GCMC simulation on adsorption...
-
What I meant to convey was there is no theoretical maximum allowed value of NUMAX, just however big you need. Clearly that is confusing so I will think about how to reword some of that section. You can find preproc.h in the Source directory. Just search for the NUMAX in there and set the value that follows it to something slightly larger than your bigest molecule. Marcus
-
Hi, thank you for your reply! The comment on NUMAX is attached in image below. May I know how do i access the preproc.h file? Regards, Rafie
-
Yes, you need to make sure NUMAX in preproc.h is larger than the biggest value of nunit in towhee_input. You will then need to recompile the code with that new value. The only comment I could find about NUMAX in the basic connectivity map manual at http://towhee.sourceforge.net/inpstyle/inpstyle_2.html was nunit (integer) The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX. Where did you see the comment about no maximum number on NUMAX? thanks, Marcus
-
Hi, I have a problem with my simulation as the size of the system is quite big. I have an error that says: READTOWHEE: nunit exceeds NUMAX set numax higher in preproc.h When i check the Towhee manual on 'basic connectivity map' section it says that there is no maximum number on NUMAX. So i'm a bit confused, do i need to update the preproc.h file or not? If yes, how do i access this file? Thank you very much! Refards, Rafie
-
Hi, I am new to Towhee and I want to know the precision of Ewald summation in the electrostatic interaction is given in which unit? In the input file manual there is a parameter, "ewald_prec" which should be 1d-4 or 1d-5. May I know what is the physical meaning of the "ewald_prec" parameter and the unit is calculated either in Kelvin or kJ/mol? Thank you! Regards, Rafie
-
Hi, By trying to make certain sites of a porous material inaccessible to adsorbate molecules, i've introduced dummy atoms with no electric charge and a considerable mass in these sites in order to simulate an isotherm of adsorption in the NPT set. Each time the simulation is started, it stops after a few steps due to the hard intermolecular overlap. How should I fix this problem to avoid this overlap? Thank you in advanced, best regards. NB : in attachement, the input file, the output file, & the...
-
hi suren, could you explain how you solve the issue? I wanted to simulate a graphene structure that i develop from gromacs and use it in towhee but i kept on getting this error: Initial Energies for Box 1 " intermolecular overlap rijsq rminsq 5.048709793414476E-029 0.250000000000000 rij: 7.105427357601002E-015 rmin: 0.500000000000000 chain, unit 1 1 i-pos 1.40000000000000 1.65000000000000 0.000000000000000E+000 jchain jj 8 1 j-pos 1.40000000000000 1.65000000000000 7.105427357601002E-015 getatompos...
-
Trying to narrow down why you are seeing different results. Here are some things I noticed about your Towhee simulations 1) You are spending 25% of the moves on performing rotations. Those moves do not do anything for single-atom molecules like Ni and H. That is why there is 100% acceptance rate as rotating an EAM atom does nothing to the simulation. You would be better served spending that time on Translations. 2) The simulation has not finished equilibrating during this first run. You can tell...
-
Namrata Masli posted a comment on discussion Help
Hello I tried running the simulation using the above conversion for chemical potential in Towhee and still I got different hydrogen intake as compared to lammps. Results from lammps seem to agree with the experimental ones. I am new to towhee so kindly help me know why am I not getting similar results from Towhee.
-
No. From a theoretical point of view I believe a system is in its lowest energy state at 0 K so not completely sure an ensemble of states has any useful meaning. From a practical point of view, all of the enegy states are scaled by 1/kT so zero temperature results in dividing by zero. If you are just trying to do a minimization I suppose you could set a very low temperature, but Towhee is not well suited for minimizations so the results are almost certain to hit a local minimum instead of a global...
-
Is it possible to simulate a system with temperature of 0 Kelvin? thanks!
-
Intake of Hydrogen increasing beyond your reservior is more a problem with the simulation having more absorption that you expected as opposed to a problem with Towhee. Clearly you need to set the value higher until there is some left over that is not absorbed. For the chemical potential conversion there is an EV to Kelvin conversion factor in Towhee of CON_EVTOK = 11604.449d0 that might help you convert your units. Marcus
-
Yes, the order of the atoms in your towhee_coords file should match the order of the atoms in towhee_input. The towhee_initial file is only used when linit is set to false. If you are reloading from a towhee_coords file after running in MD it is mostly the same as starting a new simulation (linit set to true) but you are correct that you will want to make sure the box sizes match up properly as that is not read from towhee_coords. Marcus
-
The Lennard-Jones potential, like the majority of van der Waals type potentials, has an attractive terms that scales as 1/r^6 and that continues to create some attractive forces/energy all the way out to infinity. Correspondingly, the repulsive 1/r^12 term also has a small contribution out to infinity, but it scales down substantially faster than the attractive part. The two way of handling long range interactions are 1) Just scale the potential to be zero at the cutoff and define it to be zero past...
-
Hi, I am wondering the difference of calculation of pressure with different LJ potential modifier, either shift or tail-correction. In my output file there are virial pressure and virial P_tail printed. For shifted LJ, the P_tail is 0 and with tail-correction there is a value printed out. I wonder if the total pressure of the system is the summation of the virial pressure with P_tail or not? And what is P_tail specifically? Thank you!
-
Hi, I want to start a simulation from a towhee_coords file. If my water molecules in the towhee_coords file is in the O-H1-H2 sequence, does the sequence in towhee_input (basic connectivity map) should follow the same sequence? Does the forcefield file have any effect on the atom sequence? Second, if I use towhee_coords file as starting configuration for my simulation, does having towhee_initial file with linit as True will disregard the towhee_coords file? In my case, my simulation from Towhee is...
-
Hello, I am trying to insert hydrogen into nickel using gcmc. I am facing the following problem- when I increase nsteps, the intake of hydrogen in nickel keeps on increasing and it crosses the amount of nickel atoms. This value changes with the number of hydrogen atoms(reservoir) which I have pre defined. So how do I set the initial value of hydrogen atoms and how is it related to the intake? Also, I am facing problems with the value of input chemical potential. I calculated some values of chemical...
-
Thaer AL-Jadir posted a comment on discussion Open Discussion
Hi Towhee users, I'm going to build a PC to run molecular simulations using Towhee code. What is the best PC details (system requirements) for running Towhee? Such as Processor (CPU) type, Processor (CPU) Speed, RAM, Hard Drive , etc. I'm trying to run the jobs with fast PC to speed up the calculations. My research work is on sorption: for predicting fundamental properties, such as gas sorption isotherms on various materials, including zeolites, carbon nanotubes, silica gel, and activated carbon....
-
preliminary 8.2.1
-
Very likely you already found the problem and that is doing insertions of large chain molecules into a fluid is difficult. The new chemical potential distribution tools added in version 8.2.0 might help break down the issue. For best sampling, we would be getting a nice bell curve of chemical potentials centered around the reported mean. More likely, the sampling is poor and we have a lot of zero results from failed attempts, and a handful of nonzeros. In that case we really need to improve the sampling...
-
You are running using an older towhee_input file and it is getting a bit confused and skipping past all of the move information. It then complains because without any move information, it doesn't see you having a complete set of probabilities for performing Monte Carlo moves. If you are still having problems like this let me know and I can help you get your files updated for the current version. Marcus
-
Since the box has periodic boundaries the effect will still be in the box, but I understand how it is more satisfying to have all of the coordinates in their proper location. It seems like what you are doing should work, so in order to figure out what is going wrong I would need access to the towhee_input file and any other files you are using to set up the simulation. If you are still having this problem and want to send me those files I can take a look at it. Marcus
-
schedule.F is the routine that sets up all of the logic for CBMC growth patterns. rosenbluth.F is the main routine for running a CBMC growth. The details of how to generate trials during that procedure depend on the many customizable options for the CBMC moves, most of which are hidden behind some defaults as the majority of the time people do not want to know the details and just want something that works. A combination of the Towhee manual, and some of the papers I have written about the details...
-
I am a biased source to ask about chemical potential because I have found it not to be trustworthy in many situations over the years so I try very hard to use ensembles where I do not need the value of the chemical potential and just compute it as an additional check on whether things look equilibrated. For any of the larger molecules you will hit a point where the density is sufficiently high that the chemical potential becomes very noisy. Even when using the Gibbs ensemble you have a related issue...
-
I think you have an extra space in the Atom Names in the bonded section of that file. Should be a10,1x,a10 (so 10 characters for the name, one space, and 10 characters for the next name). Looks like yours has an extra space in between which probably means the code is reading it in as ' HW' instead of as 'HW'. Would need the towhee_input file to debug it for sure. Marcus
1 >