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

Teemu Murtola teemu.murtola at gmail.com
Tue Sep 1 20:38:56 CEST 2015

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,

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
> comes to close to (less than 0.4 nm) that amino acid during the
> 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
identify methanol molecules that meet your criteria, then run gmx distance
those index groups (you need to do a per-frame analysis, e.g. loop the


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