Pressure problem when using restart file

From: Jacob Poehlsgaard (mail_lists_at_hardcoil.net)
Date: Tue Feb 06 2007 - 10:11:53 CST

Dear NAMD users

  I'm trying to equilibrate a small system of a protein and a small
ligand (SAM) in water, aiming for an NVE simulation. As part of the
equilibration, I run a 100.000 step simulation with langvin pressure
control. This is then switched off and, runs for a further 100.000 steps.

  After the control is switched off the pressure starts to fluctuate
around 1 bar, which I assume this is normal behavior.

  The problem comes when I want to continue the simulation from the
restart files. When I do this, the pressure rises to around 220 bar
within a few thousand steps (starting at 0) and fluctuates around that
instead of 1. I'm confused as to why this is happening. I thought that
when using restart files like this, it would be little different from
just continuing the simulation, and from the previous NVT run I thought
the system was well equilibrated.

  I may be missing something very basic, since I've had to attempt
learning NAMD as I go.

  On a slightly different note: Is it actually necessary to run a
simulation in NVE? I'm having a hard time finding any literature that
explicitly explains which ensemble to use, but from reading this list I
concluded that NVE is "the right way".

Jacob Poehlsgaard
PhD student
SDU, Denmark

  Here is the script with the problems:

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

set basename sub_sam

structure structures/${basename}_i.psf
coordinates structures/${basename}_i.pdb
#coords are ignored anyway as we use restart files.
binCoordinates output/2_heat/${basename}_heat.coor
binVelocities output/2_heat/${basename}_heat.vel
extendedSystem output/2_heat/${basename}_heat.xsc
firsttimestep 0
set temperature 310

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters /people/disk2/jacobp/MD/common/par_all27_prot_na.prm
parameters /people/disk2/jacobp/MD/common/par_all27_SAM.prm
wrapWater on
wrapAll on

##############################################
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 72
PMEGridSizeY 60
PMEGridSizeZ 64

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds none ;# testing
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 20

# Output
outputName /scratch/${basename}_equil
restartfreq 2000
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000

#############################################################
## Enemble Controls ##
#############################################################

##############################
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

#############################################################
## EXECUTION SCRIPT ##
#############################################################

#Run
run 500000

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