From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Mon Jun 06 2011 - 08:07:38 CDT
Hi all,
I am a newbie to NAMD. Right now i am trying to equilibrate water box.
I am not using the CHARMM forcefield. Hence i defined my own parameter file.
However when i tried to equilibrate or minimize the water i am getting the error
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Herewith, i have attached the config file. Could someone let me know how can i proceed.
structure water.psf
coordinates water.pdb
set temperature 300 ;# Tcl variable
set outputname water-equi ;# Tcl variable
temperature $temperature ;# intialize velocities randomly using Boltzmann Distribution
firsttimestep 0
## Input and ForceField Parameters ##
paratypeCharmm off
parameters clayff-namd.inp
if {0} {
cellBasisVector1 31.212 0.0 0.0
cellBasisVector2 0.0 27.000 0.0
cellBasisVector3 0.0 0.0 30.000
cellOrigin 0.0 0.0 0.0
}
##exclude scaled1-4 ##
##1-4scaling 1.0 ##
cutoff 12.0
##switching off ##
## swtichdist 10.0 ## to be used when switching is on ##
pairlistdist 14.0 ;# cutoff + 2 in general
wrapAll on
## Integrator Parameters ##
stepspercycle 2 ;# redefine pairlists every this many timesteps
timestep 1.0 ;# 1 fs/step
rigidBonds all ;# to keep the water molecules rigid
nonbondedFreq 1 ;# no. of timesteps used to calculate nonbonded interactions
fullElectFrequency 1 ;# no. of timesteps used to calculate electrostatic interactions
## Constant Temperature Control ##
langevin on ;# Uses langevin dynamics for controlling T (or) P
langevinDamping 1.0 ;# Damping Coefficient in pico seconds
langevinTemp $temperature ;# random noise at this level
langevinHydrogen no ;# no coupling of hydrogens
## Constant Pressure Control is done by the use of the langevin dynamics (see manual) ##
## Particle Mesh Ewald ##
PME yes
PMEGridSpacing 1.0 ;# Alternatively we can specify the PMEgrid Manually in case direction ##
#################################################################
### Output Options ###
#################################################################
outputname $outputname
restartfreq 500
dcdFreq 500
xstFreq 200
outputEnergies 100
outputPressure 100
###################################################################
### IMD Settings ###
###################################################################
if{0} {
IMDon on
IMDport 3000 ;# Enter this port number in VMD ##
IMDfreq 1 ;# send every 1 frame ##
IMDwait no ;# wait for VMD to connect before running ##
}
###################################################################
### Execution Script ###
###################################################################
## Minimization ##
if {0} {
minimize 100
reinitvels $temperature
}
run 100000
Thanks in advance
Naresh
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