RE: The water box shrinks at the start of the MD simulation

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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