Problems with minimization

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Sat Nov 15 2008 - 10:57:23 CST

Hi everybody,
I am running 10000 minimization steps for the Beta chain of fascin in a
water box. The simulation appears to run properly and terminates
successfully. But when I look at the dcd file, the water box is collapsed
from the first frame. I generated the psf file through the automatic psf
generator in VMD and solvated it using the solvate package (I followed the
tutorial for ubiquitin). Also, I don't get a log file as an output; I don't
understand why.

Does anybody know why this is occurring? The configuration file is copied
below. Let me know if you have any questions.

Thank you,
Diego A. Vargas
_________________________________________________________

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

structure ***
coordinates ***

set temperature 310
set outputname ***

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

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

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all
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
cellBasisVector1 48. 0. 0.
cellBasisVector2 0. 58. 0.
cellBasisVector3 0. 0 46.
cellOrigin 62. 89. 10.

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 50
PMEGridSizeY 50
PMEGridSizeZ 50

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

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

# Minimization
minimize 10000

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:38 CST