[gmx-users] shuffle and sort???
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 23 12:09:01 CEST 2003
On Tue, 2003-09-23 at 11:57, Arvid Soederhaell wrote:
> Dear all
> I have just encountered a problem with the -shuffle and -sort flags for
> grompp for MPI runs. I started my simulation on a single node, and then I
> went over to run in paralell (2 nodes). I have just realized that the
> molecules appear in a new order in the output .gro file (from the
> paralell run) than in the output from the single node run. This cause a
> big problem in reading and processing the trajectory, and also restarting
> the simulation, since the topolog doesn't match the gro-file any more.
> I guess this has to do with -shuffle and -sort but I don't know...
> What has happened is that before the paralell run I have first 64 DPPC
> molecules and then the water listed in the gro file (and in the top file).
> After the paralell run I have 32 DPPC molecules, then half of the water,
> and then another 32 DPPC molecules followed by the remaining water.
> For this system I cannot calculate the membrane order parameters, for
> example, because the atoms have different numbers in the single-node and
> multiple-node output...
> How to get this right again????
Actually deshuffle should work, see some old posts on the mailing list.
Desort is not trivial..
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Dr. David van der Spoel, Dept. of Cell & Mol. Biology
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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