[gmx-users] deshuf.ndx doesn't work for forces?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 24 08:42:26 CET 2008

LuLanyuan wrote:
> Hello All,
> I found sth like a bug regarding the deshuffle index file. I did a simulation using multiple cpus and -sort -shuffle options. After that I tried to use the deshuf.ndx file to recover the original atom order for my trr file by trjconv -n deshuf.ndx ... command. But by checking the output trr using the gmxdump, I found the oders of x and v were deshuffled while the f oder remained unchanged. In another word the values of forces were not consistent with those of positions and velocities in the new trr file.
> Is this a bug? And is there anyway to get the correct oder for forces also?
Sounds like a bug. The only way is to edit src/tools/gmx_trjconv.c.
Please file a bugzilla with an appropriate patch.

> Thanks a lot.
> Lanyuan Lu
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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