[gmx-users] g_mindist , trajectory only CA atoms, to small values?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Dec 2 08:56:02 CET 2009

Hi Peter,

> Instead of the pairs with the shortest distance a much further pair is selected. Although the output pair from "atm-pair.out" has a distance of more then 100 Angstrom the value in  the file "mindist.xvg" is smaller then one Angstrom.

Periodic Boundary Conditions?

You mention in another post that removing the header solves your
'bug'. The way you express yourself indicates you haven't got a clue
what you've removed. Dangerous... Bad idea. You've probably removed a
line which started with CRYST1, preceded by a line REMARK This is a
simulation box, or something along those lines. Sure, if you remove
PBC that way, no gromacs utility will ever see that things should be
close to each other. But you're the one that's mistaken, not the
program. Don't let yourself be mislead by visualization programs.

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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