[gmx-users] moving from single node to 2 node mdrun

hadas hadas.lapid at weizmann.ac.il
Mon Jun 27 09:39:08 CEST 2005

I am looking for a way to restart an mdrun on 2 nodes when it was 
formerly performed on a single node.
I changed the original full.tpr file into another one with 2 nodes 
(e.g. full_np2.tpr) using grompp as follows:
% grompp -v -f full.mdp -o full_np2.tpr -c after_pr.gro -p ion.top -np 2
with all other parameters retained similar to the original run (i.e. 
the original mdp file and the former .gro and top files ) and then feed 
the transformed full_np2.tpr into a new tpr file we wish to make for 
the continuation run (in this example: full_afterCrash1.tpr):
% tpbconv -f full.trr -s full_np2.tpr -time 6150 -until 10000 -e 
full.edr -o full_afterCrash1.tpr
and finally feed the renewed tpr file into the mdrun and restart the 
mpi mdrun -np 2 as usual:
% mdrun -v -np 2 -s full_afterCrash1.tpr -deffnm full_1 -c after_full_1 
 > & full_1.job
Is it the proper way to do it this or should I be expecting 
troubleshoots in the outcome?
Thanks in advance,

Hadas Lapid
Department of Biological Chemistry
Weizmann Institute of Science
Rehovot 76100, Israel.
hadas.lapid at weizmann.ac.il
Tel. :
+972-54-4984207 mobile
+972-8-9343199 work
+972-8-9344118 Fax
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