From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Jul 22 2015 - 00:27:02 CDT
Dear Richard,
Here is my config file, please have a look:
#############################################################
## JOB DESCRIPTION Equilibrate ##
#############################################################
structure solvate_6+ions.psf
coordinates solvate_6+ions.pdb
set temperature 300
set outputname equilibrate_6
# continuing a job
set inputname minimize_6
binCoordinates $inputname.restart.coor
extendedSystem $inputname.restart.xsc
#binVelocities $inputname.restart.vel
firsttimestep 0
# Input
paratypecharmm on
parameters ../par/par_all22_prot.inp
parameters ../par/par_all27_prot_lipid.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 1.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
#cellBasisVector1 52.0 0. 0.0
#cellBasisVector2 0.0 52.0 0.0
#cellBasisVector3 0.0 0 216.0
# cellOrigin 31.0 29.0 17.5
wrapAll off
wrapWater on
wrapNearest on
commotion on
dcdUnitCell yes
# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
}
# PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0
#manual grid definition
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 120
PMETolerance 0.000001
margin 6
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 200
outputPressure 200
if {1} {
fixedAtoms on
fixedAtomsFile fixed_6.pdb
fixedAtomsCol B
fixedAtomsForces off
}
constraints on
consexp 2
consref restrain_6.pdb
consKFile restrain_6.pdb
conskcol B
selectConstraints on
selectConstrX off
selectConstrY off
selectConstrZ on
run 100000
##############################################
Thanks
Abhi
________________________________
From: Richard Overstreet <roverst_at_g.clemson.edu>
Sent: Wednesday, July 22, 2015 2:05 PM
To: namd-l_at_ks.uiuc.edu; Abhishek TYAGI
Subject: Re: namd-l: wrapping in NVT
Abhi,
Are you constraining (fixing) or harmonically restraining the atoms? I use the following in my config file to fix the graphene monolayer.
fixedAtoms on
fixedAtomsFile <system pdb file>
fixedAtomsCol B
I have also found the graphene can appear to move if the periodic ABC vectors are not correct.
-Richard
On 07/21/2015 10:59 PM, Abhishek TYAGI wrote:
Hi,
I am trying to simulate water and NaCl on top of graphene sheet. While performing equilibrium (NVT) I faced following problems:
1. wrapall on
The graphene sheet moves to the next grid at the top
2. wrapWater on
wrapAll off
The ions moves out of the box
The graphene sheet is fixed and restrained. I tried different combinations of wrapping during equilibrium run, but still ions are moving out of the box.
Could you please suggest me, how to solve this.
Thanks in advance
Abhi
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