Re: water equilibration

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Fri Aug 05 2011 - 09:32:23 CDT

Need the topology and parameter files to get to the bottom of this.
Jeff

On 8/5/2011 6:41 AM, Narasimhan LOGANATHAN wrote:
> 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
>

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_chem1.eng.wayne.edu
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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