[gmx-users] g_mindist -pi (minimum periodic) and dodecahedron

[chris.neale at utoronto.ca]

I have an alanine dipeptide in a box (gromacs-3.3.1). When that box is  
cubic (3. 3. 3.), g_mindist -pi works as I expect it to (i.e.  
selecting Protein yields 2.3nm, which is what I would expect for box  
length minus end to end peptide distance; and selecting a single atom  
yields 3.0nm).

However, when the box type is a rhombic dodecahedron, I get the same  
g_mindist -pi minimum periodic distance output whether I select  
"Protein" or just a single atom of that protein. When that box is  
created by editconf -bt dodecahedron -d 1.110755, I get a box =  
{3.00000   3.00000   2.12132   0.00000   0.00000   0.00000   0.00000    
1.50000   1.50000}, and I get a g_mindist -pi minimum periodic  
distance of 2.12132 for a selection of the entire protein of just a  
single atom (or backbone, C-alpha, etc.)

For clarification, my protein is not entirely linear and I therefore  
suggest that this is some type of error.

When I further solvate the system and select SOL for g_mindist, the  
result is 0.136nm. When I select only a single SOL (4 atoms) or only  
the OW atom within that SOL molecule, I again get 2.12132nm. When I  
select two solvent residues (8 atoms) I again get 2.12132nm.

Thanks for any insight that anybody can offer. One reason that I can't  
figure this out any further myself is that I don't really understand  
the transformations involved in triclinic box PBC and VMD won't render  
all 3 axis positions correctly in periodic display (i.e. there is  
always an offset in at least one dimension, even when using trjconv -ur)

My commands were like this:
1. pdb2gmx -f a.pdb -o a.gro -p a.top -ff oplsaa -water tip4p
2. editconf -f a.gro -o b.gro [(-bt cubic -box 3. 3. 3.) ~OR~ (-bt  
dodecahedron -d 1.)]
3. make_ndx -f b.gro -o b.ndx < file_selecting_a_single_protein_atom
4. g_mindist -f b.gro -n b.ndx -pi

The input pdb file that I used was:

ATOM     13  C   ALA     2       1.199   4.163  -0.186  1.00  0.00           C
ATOM     14  CA  ALA     2       1.936   3.140  -1.094  1.00  0.00           C
ATOM     15  CB  ALA     2       1.931   3.622  -2.546  1.00  0.00           C
ATOM     16  H   ALA     2       1.473   1.194  -1.741  1.00  0.00           H
ATOM     17  HA  ALA     2       2.957   3.060  -0.751  1.00  0.00           H
ATOM     18  N   ALA     2       1.315   1.824  -1.006  1.00  0.00           N
ATOM     19  O   ALA     2       0.786   3.836   0.926  1.00  0.00           O
ATOM     20 1HB  ALA     2       2.493   4.541  -2.623  1.00  0.00           H
ATOM     21 2HB  ALA     2       0.913   3.796  -2.865  1.00  0.00           H
ATOM     22 3HB  ALA     2       2.381   2.871  -3.177  1.00  0.00           H
ATOM     23  C   ALA     3      -0.332   7.289  -1.163  1.00  0.00           C
ATOM     24  CA  ALA     3       0.299   6.426  -0.037  1.00  0.00           C
ATOM     25  CB  ALA     3       1.277   7.267   0.787  1.00  0.00           C
ATOM     26  H   ALA     3       1.377   5.531  -1.610  1.00  0.00           H
ATOM     27  HA  ALA     3      -0.451   6.044   0.639  1.00  0.00           H
ATOM     28  N   ALA     3       1.015   5.356  -0.716  1.00  0.00           N
ATOM     29  O   ALA     3       0.349   8.097  -1.795  1.00  0.00           O
ATOM     30 1HB  ALA     3       1.003   8.309   0.718  1.00  0.00           H
ATOM     31 2HB  ALA     3       2.278   7.132   0.405  1.00  0.00           H
ATOM     32 3HB  ALA     3       1.240   6.953   1.819  1.00  0.00           H
END






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