From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Mar 01 2011 - 02:56:29 CST
Forgot to add:
NAMD night build of yesterday Debian GNU/LINUX amd64
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Mar 1, 2011 at 9:54 AM
Subject: binaryrestart/binaryoutput problem
To: NAMD <namd-l_at_ks.uiuc.edu>
Hello:
To restart from previous namd run, I have to set "binaryrestart yes"
only in the .conf file. With both
binaryrestart yes
binaryoutput no
(i.e., getting .coor and .vel files as PDB)
Fatal error on PE 0> FATAL ERROR: Incorrect atom count in binary file
min-01.restart.coor
I see the issue on past post to namd, however I could not solve here.
The initial minimization conf file reads (it is a trial but it works
also for long minimization):
#############################################################
## JOB DESCRIPTION ##
#############################################################
# System mod21-popc TIP3-water-solvated, NaCl isotocic
# Min/equil with protein fixed, PME, Const. vol.
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
margin 0
structure /home/francesco/mod21-popc_md/mod21-popc-tip3-iso.psf
coordinates /home/francesco/mod21-popc_md/mod21-popc-tip3-iso.pdb
outputName /home/francesco/mod21-popc_md/min-01.restart
binaryrestart yes
binaryoutput no
set temperature 0
seed 12359
# Continuing a job from the restart files
if {0} {
set inputname min-01
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 /home/francesco/mod21-popc_md/par_all27_prot_lipid.prm
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 120.7 0. 0.
cellBasisVector2 0. 117.7 0.
cellBasisVector3 0. 0. 166.3
cellOrigin 0.008404 -1.326473 -7.952069
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5 ;# cutoff +3.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs/step
rigidTolerance 0.000001
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 4 ;# PME only every four step
stepspercycle 20 ;# redo pairlist every twenty steps
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
reproduces viscosity of water
langevinTemp $temperature ;# random noise at this level
langevinHydrogen no ;# don't couple bath to hydrogens
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile /home/francesco/mod21-popc_md/mod21-popc-tip3-iso.fix
fixedAtomsCol B
fixedAtomsForces on
}
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {1} {
minimize 20
}
Thanks for help
francesco pietra
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