Hi Reid, thanks a lot for sharing your experiences with g_mindist -pi and non-cubic boxes! Yesterday, this exact problem caused me a lot of trouble! : )
Best, Jens 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. > 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 > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
