Re: water equilibration

From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Tue Aug 02 2011 - 08:42:11 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 following error.

However i have defined the splitPatch hydrogen in the file.

Could someone kindly help me to overcome this.

Herewith, i attach my files for information

#######################################################
## Simulation of Bulk Water ##
#######################################################

## Minimization and Equilibration of Water Box ##

#######################################################
## Adjustable Parameters ##
#######################################################

structure water.psf
coordinates water.pdb

set temperature 300 ;# Tcl variable
set outputname water-equi ;# Tcl variable

## starting from scratch ##

temperature $temperature ;# intialize velocities randomly using Boltzmann Distribution

firsttimestep 0

#######################################################
## Simulation Parameters ##
#######################################################

## Input and ForceField Parameters ##
paratypeCharmm off
parameters clayff-namd-1.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 none
## 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 10 ;# redefine pairlists every this many timesteps
timestep 1.0 ;# 1 fs/step
rigidBonds water ;# 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
splitPatch hydrogen

## Constant Temperature Control ##
langevin on ;# Uses langevin dynamics for controlling T (or) P
langevinDamping 2 ;# 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
 

Regards
Naresh
 

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