[gmx-users] Continue run after a crush
feenstra at few.vu.nl
Thu Jun 23 16:27:35 CEST 2005
itai bloch wrote:
> Hi all,
> I had a 30ns simulation on 4 nodes but it crushed after ~24ns.
> I am now trying to continue the remaining time on different machine
> (both are Linux).
> I have followed the orders I found in the FAQ (in the gromacs site),
> BUT I am having doubts regarding the constraints!
> The only constraints I used were the "all-bonds" constraints in the
> original run and now after the crush the procedure I followed was:
> 1. tpbconv_mpi -s before.tpr -f before.trr -n deshuf.ndx -o crush1 -time 24411
> 2. mdrun - s crush1 .......
> Is it OK to do it like that or should I do it differently and regards
> the constraints in a different way?
Don't use deshuf.ndx, the tpr and trr files both have the atoms in the
There is nothing special about the constraints that you need to take
Normally, you don't need the -time option, tpbconv will use the last
complete frame in your .trr.
* NOTE: New Phone & Fax numbers (below) *
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
More information about the gromacs.org_gmx-users