From: Faezeh Mottaghitalab (faezeh.mt258_at_gmail.com)
Date: Wed Jan 01 2014 - 05:19:11 CST
Hello
I'm trying to simulate Bacteriorhodopsin with the NAMD 2.9 in unix.
first of all i have been omitted the retinal group of the protein from the
pdb file and i have gain the files for the 1-2 sphere, 1-3 box and 1-4
gbis ( to explain better i preferred to write the steps same as tutorial
file 'ubq').
i'm now in the 2-4 temp step and the problem is i get error 'segmentation
fault' in this step and can't understand what is the problem.
first i guess that maybe the dcd , vel ,xsc files haven't been created
correctly but i have tested again and again different namd-tutorial-files
and get the same error (segmentation fault)!
the pdb id of the bacteritodopsin that i'm using is : 1AP9
and here is my configuration file :
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Equilibration of Ubiquitin in a Water Sphere
# Use for calculating temperature fluctuations
# WARNING: DOES NOT SAVE DCD (and normally you need it)
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/ap9_2_ws.psf
coordinates ../common/ap9_2_ws.pdb
set temperature 310
set outputname ap9_2-nve
# Continuing a job from the restart files
if {1} {
set inputname ../1-2-sphere/ap9_2_ws_eq
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}
firsttimestep 0
#############################################################
## 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
if { 0 } {
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
}
# Output
outputName $outputname
#restartfreq 50 ;# 500steps = every 1ps
#dcdfreq 50
outputEnergies 50
outputPressure 50
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 16.626047134399414, 39.246639251708984,
6.797718524932861
sphericalBCr1 26.0
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
# minimize 900
# reinitvels $temperature
run 5000 ;# 1000ps
thanks in advance,
faezeh
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