Re: MD in a loop with different names for dcd files

From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Tue Mar 14 2006 - 11:44:46 CST

Correction to the email:

"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-4."

===================================================
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
===================================================

On Tue, 14 Mar 2006, Himanshu Khandelia wrote:

> 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]
> }
> ##########################################
>
>
> 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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