From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 13 2011 - 08:21:18 CST
On Tue, Dec 13, 2011 at 9:10 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
> Dear Namd Users,
>
> I run 5 ns md simulation for water molecules with the conf file below. And I
> want to get the final coordinates of all water molecules in defined cell
> sizes ( 40 40 65 ) . How can I do this operation in NAMD ?
don't use a flexible cell?
axel.
>
> Thank you very much for your help.
>
> Regards.
>
> *********
> #--- This is a test namd configuration file
>
> paratypeCharmm on
> parameters water.prm
>
> structure water.psf
> coordinates water.pdb
> outputName water_1out
>
> set temperature 300
> temperature $temperature
>
>
> firsttimestep 0
>
> # Integrator Parameters
> timestep 1
> nonbondedFreq 1
> fullElectFrequency 5
> stepspercycle 10
>
>
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.8333333
> cutoff 19.7
> switching on
> switchdist 17
> pairlistdist 24
>
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen on ;# don't couple langevin bath to hydrogens
>
>
> #--- PBC
>
>
> cellBasisVector1 40. 0.0 0.0
> cellBasisVector2 0.0 40. 0.0
> cellBasisVector3 0.0 0.0 65.
>
> #--- PME
>
> dielectric 1
> PME on
> PMEGridSizeX 45
> PMEGridSizeY 45
> PMEGridSizeZ 72
>
> # Constant Preswaterre Control (variable volume)
> useGroupPressure no
> useFlexibleCell yes
> useConstantArea yes
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
>
>
> #--- Output & Restart
>
> binaryoutput no
>
> binaryrestart yes
>
> restartname water_restart
> DCDfile water_out.dcd
>
>
> restartfreq 1250
> dcdfreq 1250
> xstFreq 1250
> outputEnergies 1250
> forceDCDfreq 1250
> outputPressure 1250
> outputtiming 1250
>
> minimize 12500
> reinitvels $temperature
>
> run 5000000
>
> *************
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:03 CST