MD in a loop with different names for dcd files

From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Tue Mar 14 2006 - 10:56:21 CST

Hi,

I want to run an MD in NAMD, such that I get a new trajectory file every
100 ps, with a new name. For example, the trajectory names would be like:

system-1.dcd # this trajectory is for 0-100ps
system-2.dcd # this trajectory is for 100-200ps
system-3.dcd # this trajectory is for 200-300ps
...

For this I tried to use the following loop in the config file.

##########################################
set start 20
set I 1;
while { $I < 5 } # stop after 4 runs thru the loop <=> 400 ps
{
  outputname system-${I}
  firsttimestep $start
  run 50000 # run for 100ps
  set I [expr $I + 1]
  set start [expr $start + 50000]
}
##########################################

However, I still get only one dcd file name system-1.dcd (containing the
entire trajectory), and I get .vel, .xsc, and .coor file with the prefix
system-3.

Can someone please tell me where I am wrong? Thank you !

-Himanshu

===================================================
Himanshu Khandelia

Doctoral Candidate,
Kaznessis Research,
Department of Chemical Engineering and Materials Science,
University of Minnesota

Mailing Address:

499, Walter Library,
117, Pleasant St. SE,
Minneapolis, MN 55455

Phone(o): 612-624-4945
===================================================

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