Tutorial-l Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 11 2008 - 09:01:57 CDT

Hi Saravana,
all that you should need to add to this script is a set of lines telling
namd where to find your psf and an initial coordinate file, and the
periodic system to use. So, for example, you could add to the top of the
file

structure 1ubq.psf
coordinates 1ubq.pdb
temperature 300
parameters par_all27_prot_na.inp

cellBasisVector1 127 0 0
cellBasisVector2 0 128 0
cellBasisVector3 0 0 83
cellOrigin 0 0 0

(obviously, replacing these parameters with those appropriate for your
system)

You also need to change the name of the dcd file used in the script to
match the one you actually want to analyze.

Best,
Peter

saravana prakash wrote:
>
> Hi,
>
>
> I like to see the namd pressure profile for my system. whereas i
> attached the following the script which i found from the namd
> documentation, explains how to calculate the pressure profile.
>
> how to start the beginning of the simulation for this half script.
>
> Could you please suggest me , how to start the beginnig of the script
> for this following item.
> with complete model example would be helpful
>
> Pme on
> PmeGridSizeX 64
> PmeGridSizeY 64
> PmeGridSizeZ 64
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> switching on
> switchdist 9
> cutoff 10
>
>
> pairlistdist 11
>
> pressureProfile on
> pressureProfileSlabs 30
> pressureProfileFreq 100
> pressureProfileAtomTypes 6
> pressureProfileAtomTypesFile atomtypes.pdb
> pressureProfileEwald on
>
> pressureProfileEwaldX 16
>
> pressureProfileEwaldY
> 16
> pressureProfileEwaldZ 16
>
> set ts 0
> firstTimestep $ts
>
> coorfile open dcd pp03.dcd
> while { [coorfile read] != -1 } {
> incr ts 500
> firstTimestep $ts
>
> run 0
>
> }
> coorfile close
>
> thank you very much
>
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