[gmx-users] Small bug with -pi in g_mindist?

[David van der Spoel]

On 2013-03-07 19:02, Reid Van Lehn wrote:
> Hi users,
>
> I was experimenting with using a hexagonal unit cell for a lipid membrane
> system by building a box with vectors A A C (i.e. two equivalent vectors in
> the xy plane and distinct z vector) and angles 90 90 60, which is correctly
> represented as hexagonal after converting with trjconv. I equilibrated this
> box and a system with the same number of lipids and water molecules but in
> a rectangular box. I confirmed that after equilibration the area per lipid
> for each system is the same, and after  visualization confirmed that the
> hexagonal system and rectangular system occupied about the same area (of
> course subject to fluctuations).
>
> For a hexagon and square of equivalent area, the minimum distance between
> periodic images should be 1/sqrt( sin 60 degrees) = ~1.075 times larger for
> the hexagon than in the square case if I worked out the geometry correctly.
> To test to make sure I had the correct new minimum distance, I ran
> g_mindist -pi with both a single atom and a single water molecule from the
> simulation box after resizing the Z axis to a large value, restricting the
> minimum distance between periodic images to only the xy plane.
> Surprisingly, the result came out as smaller than the equivalent minimum
> distance in the rectangular box, and was equal to the box vector B. Since
> in GMX box vectors are stored in the .gro file in a 3x3 matrix, the
> box[YY][YY] vector for an ab angle of 60 degrees was (correctly) equal to
> sin 60 * the A vector. However, the correct periodic distance should have
> been the A  vector, which again was correctly ~1.075 * the box vector in
> the rectangular box by comparing the .gro files.
>
> I believe that this is a small bug in g_mindist, and found the source: on
> lines 71 and 92 of gmx_mindist.c (version 4.6), the initial minimum
> distance is set based on the minimum of the box[XX][XX], box[YY][YY], and
> box[ZZ][ZZ] vectors. I think this is fine for rectangular boxes, but fails
> for triclinic boxes with box angles differing from 90 degrees. In my
> particular case of a hexagonal xy plane, the box[YY][YY] vector is shorter
> than the box[XX][XX] vector by a factor of sin 60, but this is not actual
> the shortest distance. Explicitly printing out the distances calculated
> between periodic images in the current version of the code for both a
> single atom and a water molecule confirms that the minimum distance is the
> box[XX][XX] vector.

Thanks for reporting and giving a solution.

http://redmine.gromacs.org/issues/1183

>
> A fix for this was substituting norm(box[0]), norm(box[1]), and
> norm(box[2]) for the box[XX][XX] etc. vectors in line 71, as then the
> minimum was properly set.
>
> I realize this is a bug that is unlikely to affect many users, but given
> the prevalence of non-rectangular boxes and the observation of previous
> complaints about mindist in the user list, I thought it would be good to
> report.
>
> Please let me know if I made an error anywhere!
>
> Best,
> Reid
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se