## Bug #1183

### g_mindist -pi bug with triclinic boxes

**Description**

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.

### Associated revisions

### History

#### #1 Updated by David van der Spoel almost 5 years ago

**Target version**changed from*4.5.7*to*4.6.2*

#### #2 Updated by David van der Spoel almost 5 years ago

**Target version**changed from*4.6.2*to*4.5.7*

Fixed in https://gerrit.gromacs.org/#/c/2221/

#### #3 Updated by Mark Abraham over 4 years ago

**Status**changed from*New*to*Accepted***Affected version**set to*4.5.5*

#### #4 Updated by Mark Abraham over 4 years ago

**Status**changed from*Accepted*to*In Progress*

#### #5 Updated by Mark Abraham over 4 years ago

**Status**changed from*In Progress*to*Resolved*

#### #6 Updated by Rossen Apostolov almost 4 years ago

**Status**changed from*Resolved*to*Closed*

Fixes #1183 PBC bug in g_mindist

Fixes minimum size of the box if triclinic when checking

the periodic image distance.

Change-Id: I54cb593c42f791b6540147233c345069f84e2f33