Fwd: binaryrestart/binaryoutput problem

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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