From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Wed Oct 11 2006 - 14:28:41 CDT
Hi all
I am trying to restrain my protein and equilibrate the system. when i
am trying to restart my simulation, then i am getting error message like
charm++ fetal error
FATAL ERROR : Line too long in pdb file min/prodh_wb_min.restart.coor
but when i am setting my restrain off then i am able to restart the
simulation. my config file looks like.
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Sphere
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/prodh_wb.psf
coordinates ../common/prodh_wb.pdb
set temperature 100
set outputname equil100/prodh_wb_min
if {1} {
set inputname min/prodh_wb_min
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.xsc
}
firsttimestep 10000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp
#temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 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 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 -81.875 0.0 0.0
cellBasisVector2 0.0 -79.3840036392 0.0
cellBasisVector3 0.0 0.0 -81.5929965973
cellOrigin 5.72501993179 45.225315094 49.4890518188
#wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 82
PMEGridSizeY 80
PMEGridSizeZ 82
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#les off
#lesFactor 10
#lesReduceTemp on
#lesReduceMass on
#lesCol B
constraints on
consexp 2
consref $inputname.restart.coor
conskfile ../common/prodh_wb_res5.pdb
conskcol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#minimize 10000
#reinitvels $temperature
run 10000 ;# 600ps
i am not understanding the problem as i am following the manual. is there
any problem in my way of defining consref file name. i am taking coordinates
for this file from previous simulation.
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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