From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 05 2011 - 05:56:04 CDT
Hi,
where is the error?
Mit freundlichen Grüßen
Norman Geist.
-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Narasimhan LOGANATHAN
Gesendet: Freitag, 5. August 2011 12:41
An: NAMD
Betreff: namd-l: water equilibration
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
## Minimization and Equilibration of Water Box ##
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
## 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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