NAMD CONFIG FILE::

From: Asmita Gupta (asmita4des_at_gmail.com)
Date: Wed Apr 21 2010 - 12:50:51 CDT

• Next message: Peter Freddolino: "Re: building a MARTINI bilayer"
• Previous message: Edward Lyman: "building a MARTINI bilayer"
• Next in thread: Patrick Yee: "Re: NAMD CONFIG FILE::"
• Reply: Patrick Yee: "Re: NAMD CONFIG FILE::"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

• Next message: Peter Freddolino: "Re: building a MARTINI bilayer"
• Previous message: Edward Lyman: "building a MARTINI bilayer"
• Next in thread: Patrick Yee: "Re: NAMD CONFIG FILE::"
• Reply: Patrick Yee: "Re: NAMD CONFIG FILE::"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:02 CST