[gmx-users] continuations

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 17 10:56:31 CEST 2005

On Fri, 2005-06-17 at 08:41 +0100, 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.

Use tpbconv -extend instead.

> 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!
> Thanks
> Jo
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> J.F.Hanna at warwick.ac.uk
> jfhanna at gmail.com
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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