[gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

[Teemu Murtola]

You do not need such a complicated loop for using gmx distance, since you
can just provide your selections directly to gmx distance and it will
evaluate them automatically for each frame.

But for these problem you describe, gmx pairdist (new in Gromacs 5.1)
probably can give you all the distances you want with a single invocation
(you still need to compute the average from the output file).

Best regards,
Teemu

On Tue, Sep 1, 2015, 14:32 Justin Lemkul <jalemkul at vt.edu> wrote:


On 9/1/15 5:15 AM, Tushar Ranjan Moharana wrote:
> Hi Everyone,
> I have simulated a protein in 40 % methanol. Now I want to analyze the
> average distance between any amino acid and all the methanol molecule
which
> comes to close to (less than 0.4 nm) that amino acid during the
simulation.
> I tried many GROMACS analysis tool for this but I couldn't succeed. Can
> anybody kindly suggest me which analysis tool will be useful for me.
>

Use gmx select to generate index groups for each frame in the trajectory
that
identify methanol molecules that meet your criteria, then run gmx distance
using
those index groups (you need to do a per-frame analysis, e.g. loop the
calls).

-Justin