From: sunyeping (sunyeping_at_aliyun.com)
Date: Sun Jul 27 2014 - 19:19:15 CDT
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发件人：Zheng Fulu <flzheng525_at_gmail.com>
发送时间：2014年7月28日(星期一) 02:53
收件人：namd-l <namd-l_at_ks.uiuc.edu>
主 题：namd-l: The water box shrinks at the start of the MD simulation
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Dear All, My system is solvated in a water box and the whole water box is minimized by 20000 steps. Then I want to heat the whole box up to 300K. At the start of the MD simulation, the whole box shrinks obviously. My configuration file is as follows:
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ionized.psf
coordinates ionized.pdb
set temperature 300
set outputname whole_out
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 10.0
pairlistdist 16.0
# Integrator Parameters
timestep 2 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# 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 152.1 0.0 0.0
cellBasisVector2 0.0 158.9 0.0
cellBasisVector3 0.0 0.0 152.6
cellOrigin -52.6 -16.9 -29.8
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 20000
for { set TEMP 0 } { $TEMP < 300 } { incr TEMP 30 } {
reinitvels $TEMP
langevinTemp $TEMP
run 5000
}
reinitvels $temperature
langevinTemp 300
langevinPistonTemp 300
run 1000000 ;# 2ns I have found that someone said the NVT equilibration should be used in the first stage, then the NPT equilibration. Is this the right way to fix this problem? Is there anyone who has encountered this problem? The simulation is done by NAMD using the CHARMM force field. Thank you very much! Fulu Try changing "useFlexibleCell" to "no" and see what happens.
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