Tutorial-l Mailing List

From: saravana prakash (saravana_at_physik.uni-kl.de)
Date: Wed Jun 11 2008 - 07:09:44 CDT

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

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**