[gmx-users] minimum residue distances

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Dec 7 12:08:12 CET 2009

Hi Carla,

Please be specific with your questions, regardless of your level of
expertise and field. Are you after a program to calculate minimal
distances, which would be a Gromacs specific question? In that case
have a look at g_mdmat, g_mindist, g_dist. Also be sure to get current
on the use of make_ndx to generate index groups for specific
There is not a formula for calculating the minimal distance between
residues. There are algorithms, but are you really interested in
those? As for the distance itself, the square root of the sum of
squares of the differences is not specific to molecular dynamics.



On Mon, Dec 7, 2009 at 11:18 AM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi everyone,
> since i'm in beginner in molecular dynamics, I still have some trouble with
> finding the adequate formulas. Now, I'm trying to find the formula to
> calculate the minimum residue distances. I didn't find it in Gromacs manual,
> so please does anyone have an idea?
> Thanks
> Carla
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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