From: Matt Watkins (
Date: Tue Oct 13 2009 - 07:05:27 CDT

Hi all,

I'm running in to some problems writing trr files with the gromacs molfile
plugin. My cell is hexagonal, with the main symmetry axis along the z
direction. The cell vectors are read correctly, however, on writing in trr
format the cell angles become cubic and the "B" cell vectors are incorrect -
test case below.

It looks to me as if there is an inconsistency between lines 520 of
Gromacs.h and line 459 on gromacsplugin.C (but my C is terrible, I may well
be have missed other internal rotations done by VMD and I've failed to get
recompiled plugins to work with my vmd to check).

does anyone agree that the axes get distorted in the gromacs plugin, and is
the fix as simple as changing the dot product in the gromacs plugin?

How do I link recompiled molfile plugins into vmd - do I need to recompile
vmd itself?



Example problem file
Load in pdb format save in trr, reload pdb and trr and pbc get.

CRYST1 30.754 30.754 70.000 90.00 90.00 60.00 P 1 1
ATOM 1 F F X 2 29.790 11.630 8.670 0.00 0.00

p.s. apologies if this appears twice, I tried previously and think the
message got bounced.