VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Oct 04 2007 - 15:34:32 CDT

On Thu, 4 Oct 2007, Narender Singh Maan wrote:

NS> package require namdenergy
NS> set sel1 [atomselect top "segname PTO1"]
NS> set sel2 [atomselect top "(within 15 of segname PTO1) and not segname PTO1"]

set nf [molinfo top get numframes]

NS> for {set i 0} {$i < [molinfo top get numframes]} {incr i} {

for {set i 0} {$i < $nf} {incr i} {

NS> $sel1 frame 0
NS> $sel2 frame 0
NS> namdenergy -sel $sel1 $sel2 -vdw -skip [molinfo top get numframes] -par
NS> par_all27_prot_na.prm -extsys x.xsc -ofile elect1-$i.dat -switch 10 -cutoff
NS> 12
NS> animate delete end 0
NS> }
NS> ...........................................................................................................................................................................

NS> 2) Also from this script, in the output i get only half the number of VDW
NS> energies, compared to the number of frames i have in my dcd file (i.e.
NS> "molinfo top get numframes" is 100 but i only get 50 VDW values in my
NS> output)!!

no surprise there. this is because of the strange way you construct the
loop. you are stepping up $i, but recomputing the number of frames
and deleting the processed frame. if you change the script as outlined
above it should work as expected.

axel.

NS>
NS> I would greatly appreciate any input form the members.
NS> thank you
NS> narender
NS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.