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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