Re: [GaMD-discuss] GaMD boost parameters (gamd-restart.dat file) issue
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Re: [GaMD-discuss] GaMD boost parameters (gamd-restart.dat file) issue
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From: Miao, Y. <Yin...@me...> - 2025-07-13 20:15:04
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Hi Arpan,
Attached I’m sending you a copy of the Pep-GaMD simulation input files we used, with the .in files pasted here:
::::::::::::::
md.in
::::::::::::::
GaMD equilibration simulation
&cntrl
imin=0, ! No minimization
irest=0, ! This IS a new MD simulation
ntx=1, ! read coordinates only
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
tempi=300.0, ! Initial temperature
temp0=300.0, ! Target temperature
ig=-1, ! random seed
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=32800000, ! simulation length
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=1, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=100, ! Print energies every 1000 steps
ntwx=100, ! Print coordinates every 1000 steps to the trajectory
ntwr=5000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
ntwprt = 1087,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling). Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
! csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
! gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
! ninterface=2, ! Number of interfaces (2 for bilayer)
! Set water atom/residue names for SETTLE recognition
!watnam='TIP3', ! Water residues are named TIP3
!owtnm='OH2', ! Water oxygens are named OH2
! GaMD parameters
igamd = 15, iEP = 2,iED=1,irest_gamd = 0,
ntcmd = 800000, nteb = 32000000, ntave = 160000,
ntcmdprep = 320000, ntebprep = 320000,
sigma0P = 4.0, sigma0D = 6.0,
gti_cpu_output = 0, gti_add_sc = 1,
icfe = 1,
ifsc = 1,
timask1 = ':58-68',
scmask1 = ':58-68',
timask2 = '',
scmask2='',
/
::::::::::::::
gamd-restart.in
::::::::::::::
GaMD production simulation
&cntrl
imin=0, ! No minimization
irest=0, ! This IS a new MD simulation
ntx=1, ! read coordinates only
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
tempi=300.0, ! Initial temperature
temp0=300.0, ! Target temperature
ig=-1, ! random seed
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=50000000, ! simulation length
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=1, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=100, ! Print energies every 1000 steps
ntwx=100, ! Print coordinates every 1000 steps to the trajectory
ntwr=5000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
ntwprt = 1087,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling). Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
! csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
! gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
! ninterface=2, ! Number of interfaces (2 for bilayer)
! Set water atom/residue names for SETTLE recognition
!watnam='TIP3', ! Water residues are named TIP3
!owtnm='OH2', ! Water oxygens are named OH2
! GaMD parameters
igamd = 15, iEP = 2,iED=1, irest_gamd = 1,
ntcmd = 0, nteb = 0, ntave = 160000,
ntcmdprep = 0, ntebprep = 0,
sigma0P = 4.0, sigma0D = 6.0,
gti_cpu_output = 0, gti_add_sc = 1,
icfe = 1,
ifsc = 1,
timask1 = ':58-68',
scmask1 = ':58-68',
timask2 = '',
scmask2='',
/
::::::::::::::
md-restart.in
::::::::::::::
GaMD restart simulation
&cntrl
imin=0, ! No minimization
irest=1, ! This IS a new MD simulation
ntx=5, ! read coordinates only
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
tempi=300.0, ! Initial temperature
temp0=300.0, ! Target temperature
ig=-1, ! random seed
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=50000000, ! simulation length
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=1, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=100, ! Print energies every 1000 steps
ntwx=100, ! Print coordinates every 1000 steps to the trajectory
ntwr=5000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
ntwprt = 1087,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling). Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
! csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
! gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
! ninterface=2, ! Number of interfaces (2 for bilayer)
! Set water atom/residue names for SETTLE recognition
!watnam='TIP3', ! Water residues are named TIP3
!owtnm='OH2', ! Water oxygens are named OH2
! GaMD parameters
igamd = 15, iEP = 2,iED=1, irest_gamd = 1,
ntcmd = 0, nteb = 0, ntave = 160000,
ntcmdprep = 0, ntebprep = 0,
sigma0P = 4.0, sigma0D = 6.0,
gti_cpu_output = 0, gti_add_sc = 1,
icfe = 1,
ifsc = 1,
timask1 = ':58-68',
scmask1 = ':58-68',
timask2 = '',
scmask2='',
/
The simulations may run as follows:
##GaMD equilibration
#~/bin/pmemd.cuda -O -i md.in -p sys.prm -c density.rst -o md.out -r gamd-1.rst -x md-1.nc -gamd gamd-1.log
##the GaMD production
~/bin/pmemd.cuda -O -i gamd-restart.in -p complex.prmtop -c gamd-1.rst -o gamd-2.out -x md-2.nc -r gamd-2.rst -gamd gamd-2.log
##GaMD restart production
~/bin/pmemd.cuda -O -i md-restart.in -p complex.prmtop -c gamd-2.rst -o gamd-3.out -x md-3.nc -r gamd-3.rst -gamd gamd-3.log
for i in `seq 4 15`
do
j=`echo $i|awk '{print $1-1}'`
~/bin/pmemd.cuda -O -i md-restart.in -p complex.prmtop -c gamd-$j.rst -o gamd-$i.out -x md-$i.nc -r gamd-$i.rst -gamd gamd-$i.log
done
Hope they help!
Best,
Yinglong
Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org<http://miaolab.org/>
Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov
On Jul 11, 2025, at 2:11 PM, Arpan Tapdiya <agt...@nc...> wrote:
You don't often get email from agt...@nc.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Hello,
I am Arpan Tapdiya, a PhD student in the Prof.Carol Hall lab at NC State University, Raleigh. I am trying to replicate Pep-GaMD method for enhanced sampling (reference article - https://doi.org/10.1063/5.0021399). While trying to run the three production runs independently for the system with PDB ID - 1CKA, I ran into a problem where the GaMD parameters are not being updated in the game-restart.dat file.
I have the production run for 1microsecond broken down into 50 parts (each of 20 nanoseconds). My game-restart.dat file has not been updated since the equilibration part. My parameters for the production and equilibration runs are attached, and the loop for the production run is being executed through the following commands -
##syntax starts here -
prev_rst="equil.rst"
for i in {1..50}; do
out="prod${i}.out"
rst="prod${i}.rst"
traj="prod${i}.nc"
gamd_data="gamd_prod${i}.dat"
echo "Running production step $i..."
${pmemd_path}/pmemd.cuda_SPFP -O -i prod.in<http://prod.in/> -o $out -p pep.prmtop -c $prev_rst -r $rst -x $traj -gamd gamd-restart.dat "${gamd_data}"
prev_rst=$rst
cp gamd-restart.dat gamd-restart{i}.dat
echo "Production step ${i} completed"
done
Can you help me solve the issue where my GaMD parameters are updated after every production step such that the simulation has a continuous bias potential?
Thank you.
Best,
Arpan
--
Arpan Tapdiya
Graduate Student
Department of Chemical and Biomolecular Engineering
North Carolina State University
<equil.in><prod.in>
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