Minimisation issue

From: venkata agasthya (kvagasthya_at_gmail.com)
Date: Wed Jul 24 2013 - 15:12:06 CDT

Hello everyone,

I have mailed in this group before about my problem with minimizing the
energy of a protein/water system. I have tried running the minimization
script using 500, 1000 and 10000 steps but the run gets stuck at a
particular step and doesn't continue. It reaches a certain step and get's
stuck. do anyone know why this happens.

This is my minimization config file

###################################################
# ESTROGEN RECEPTOR:
###################################################

# MD SETUP

timestep 2.0
numsteps 1000

# FLEXIBLE CELL

useflexiblecell no

# PSF

structure protein.psf

# FORCE FIELD

parameters /work/agasthya/testing/par_all27_prot_lipid.prm
paraTypeCharmm on

# INPUT

coordinates protein.pdb

# PBC

CellBasisVector1 50 0 0
CellBasisVector2 0 50 0
CellBasisVector3 0 0 50
CellOrigin 0 0 0

# OUTPUT

outputenergies 100
outputtiming 100
outputpressure 100
restartfreq 100
XSTFreq 100

outputname minimization_0
restartname minimization
binaryrestart yes
binaryoutput no

# PME

PME yes
PMETolerance 10e-6
PMEInterpOrder 4

PMEGridSpacing 1

# WRAP

wrapAll on

# CONSTANT-T

temperature 300.0

langevin on
langevinTemp 300.0
langevinDamping 1.0

# CONSTANT-P

LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 75
LangevinPistonDecay 25
LangevinPistonTemp 300
StrainRate 0.0 0.0 0.0
useGroupPressure yes

# SPACE PARTITIONING

splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 20
margin 1.0

# CUT-OFFS

switching on
switchdist 8.0
cutoff 9.0
pairlistdist 10.0

# RESPA

#fullElectFrequency 2
#nonbondedFreq 1

# 1-4 NON-BONDED

exclude scaled1-4
1-4scaling 1.0

# COM

commotion no

# SHAKE

rigidbonds all
rigidtolerance 0.000001
rigiditerations 400

# MINIMIZATION

minimize 1000

Thanks,
Agasthya.

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