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
===================================================
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:44 CST