[gmx-users] continuations

Joanne Hanna J.F.Hanna at warwick.ac.uk
Fri Jun 17 09:41:44 CEST 2005

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

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com

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