From: Amali Guruge (amaligg2010_at_gmail.com)
Date: Wed Nov 08 2017 - 17:17:14 CST
Thank you very much for the answer. I tried to do the simulation, but again
I got the following error.
Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
My em.conf file contains following parameters.
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
set inputname PEG_SOL
set current em
#structure $inputname.psf
#coordinates $inputname.pdb
# Set body temprature
set temperature 298
set outputname ${inputname}_$current
firsttimestep 0 #only necessary if not using catdcd
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
#paraTypeCharmm on
#parameters top_prm/par_all36_cgenff.prm
#parameters top_prm/PEG.prm
temperature $temperature
gromacs on
grotopfile C12EO6.itp
grotopfile gromos54a7_atb.ff/spc.itp
coordinates structures/C12EO6_water_rbox.pdb
# Force-Field Parameters (lowering settings adds error risk, current
settings widely used)
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters (only a few valid combinations, consult NAMD manual)
timestep 2.0 # 2fs/step
rigidBonds all # needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on # do langevin dynamics
langevinDamping 5 # damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off # don't couple langevin bath to
hydrogens
# Periodic Boundary Conditions (start size of unit cell, ignored once .xst
specified)
cellBasisVector1 152.0 0. 0.
cellBasisVector2 0. 152.0 0.
cellBasisVector3 0. 0. 152.0
cellOrigin 0. 0. 0.
wrapWater on
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
pmeGridSpacing 1.0
# Constant Pressure Control (variable volume)
useGroupPressure yes # needed for rigidBonds
# yf for membrane simulations, should switch these on
useFlexibleCell yes
useConstantRatio yes #keeps xy plane aspect ratio constant
useConstantArea no #when yes volume is fixed, still allows
stretching
langevinPiston on
langevinPistonTarget 1.01325 #in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 25000 # 500steps = every 1ps
dcdfreq 30
xstFreq 30
outputEnergies 40 # must be multiple of stepspercycle
outputPressure 40
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Interactive MD
#IMDon on
#IMDport 5678
#IMDfreq 1 #update frequency, as low as bandwidth allows
#IMDwait no #if yes, job only runs while connected
#############################################################
## EXECUTION SCRIPT ##
#############################################################
minimize 5000
reinitvels $temperature
On Tue, Nov 7, 2017 at 4:22 PM, Haohao Fu <fhh2626_at_gmail.com> wrote:
> Hi Amail Guruge,
>
> NAMD can use gromacs files directly, see https://www-s.ks.uiuc.edu/
> Research/namd/2.12/ug/node14.html
>
> You can also try Parmed (http://parmed.github.io/ParmEd/html/index.html)
> if you want to have psf and pdb files.
>
> Cheers,
> Haohao
>
> 2017-11-07 9:53 GMT+08:00 Amali Guruge <amaligg2010_at_gmail.com>:
>
>> Dear NAMD users,
>>
>> I want to simulate my system considering Gromacs force field parameters.
>> In that case how I generate the psf file? Can anyone help me?
>>
>> Thank you in advance.
>>
>
>
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