[gmx-users] Continue run after a crush

[Anton Feenstra]

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 
same order.
There is nothing special about the constraints that you need to take 
care of.
Normally, you don't need the -time option, tpbconv will use the last 
complete frame in your .trr.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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