[gmx-users] continuations

Rainer Böckmann rainer at bioinformatik.uni-saarland.de
Fri Jun 17 10:31:42 CEST 2005

use tpbconv

Joanne Hanna wrote:

>Deal All,
>As our cluster has a wall time of 12 hours I can only get 900ps out of my simulation at a time and therefore i have to do a lot of continuations. The way i have been doing this is to do a:
>grompp including -t traj.trr and -e ener.edr
>turning off gen vel and having unsonstrained start= yes in *.mdp file.
>i have then written these new files to a new directory so as not to write over the existing traj.* and ener.edr and confout.gro files. this therefore leaves me with lots of files that i can paste together using trjcat, however their start times are all 0 and therefore this does not work.
>I have got around this by altering the timing of the subsequent files using trjconv and the -t0 option, this therefore gives me files that i can paste together and actually view the whole trajectory, rmsd, energies etc.
>My questions are:
>is this an okay method, 
>if i have done 200 ps and then 500 and then 900, do i reassign the second file a start time of 201ps and the third a time of 702ps?
>is there a simplier way to do all of this!
>Joanne Hanna
>Department of Chemistry
>University of Warwick
>CV4 7AL
>J.F.Hanna at warwick.ac.uk
>jfhanna at gmail.com
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>gmx-users at gromacs.org
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Dr. Rainer Böckmann
Theoretical & Computational Membrane Biology
Center for Bioinformatics Saar
Universität des Saarlandes
Gebäude 17.1, EG
D-66041 Saarbrücken, Germany
Phone: ++49 +681 302-64169  FAX: ++49 +681 302-64180
E-Mail: rainer at bioinformatik.uni-saarland.de

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