From: Patrick Yee (pyee_at_nd.edu)
Date: Wed Apr 21 2010 - 14:34:49 CDT
Asmita,
These parameters may all be found in the NAMD user guide. 1-4 scaling
is specific to the parameters file, the cutoff is specific to how
accurate (but computationally expensive) you want calculations to be,
and rigidbonds on means you will be assuming all water molecules are
rigid (in order to make calculations faster). Again, please look in
the NAMD user guide for clarification on every parameter.
Patrick
On Wed, Apr 21, 2010 at 1:50 PM, Asmita Gupta <asmita4des_at_gmail.com> wrote:
> I am trying to generate configuration file for dna-water system using the
> following commands,but m not sure what value to give to some of the
> parameters: -
> structure "dna_wb.psf"
> coordinates "dna_wb.pdb"
> set temperature 310
> set outputname dna_wb_eq
> #firsttimestep ?
>
> paraTypeCharmm on
> parameters par_all27_prot_na.prm
> #exclude ?
> #1-4scaling ?
> #cutoff ?
> switching on
> #switchdist
> #pairlistdist
> timestep 2.0
> #rigidBonds ?
> stepspercycle 100
> langevin on
> langevinTemp 310
> outputName dna_wb_eq
> #restartfreq
> #dcdfreq
> cellBasisVector1 x=42,y=0,z=0
> cellBasisVector2 x=0,y=45,z=0
> cellBasisVector3 x=0,y=0,z=50
> #cellOrigin
> wrapWater on
> wrapAll on
> PME yes
> PMEGridSizeX
> PMEGridSizeY
> PMEGridSizeZ
> #useGroupPressure
> useFlexibleCell no
> useConstantArea yes
> langevinPiston yes
> langevinPistonTarget 1.013
> xstFreq
>
> # execution script
> minimize 100
> #reinitvels ??
> run 2000
>
> also while trying to run the config file,i am getting the following error
>>unknown command structure
>>unknown command parameter
>>unknown command paraTypeCharmm
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