[gmx-users] Listing residues in gromacs

[Subhomoi Borkotoky]

Hi Christian,

Thank you for your reply. The command worked well. I got the indices of the
residues. I want to calculate the occupancies of the residues near my
reference ion within say 0.5 nm. It will help me a lot if you could suggest
something for it. I have tried gmx distance and gmx mindist with the index
file from gmx select, but not successful.

Thanks & Regards,
--------------------------
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subhomoi at yahoo.com





On Tue, Feb 18, 2020 at 6:58 PM Christian Blau <blau at kth.se> wrote:

> Hi Subhomoi,
>
>
> Yes,
>
> gmx select
>
> can do that (see
> http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html)
> <http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html>
>
>
> For what you want to do, it's beneficial to have a look at the selection
> syntax here
>
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html
> <
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html?highlight=selection
> >
>
>
> Best,
>
> Christian
>
> On 2020-02-18 13:14, Subhomoi Borkotoky wrote:
> > Hi,
> >
> > Is there any option in gromacs to list residues/atoms around a reference
> > group? I have checked trjorder , but it only gives number of molecules.
> >
> > Thanks & Regards,
> > --------------------------
> > *Subhomoi Borkotoky, Ph. D.*
> > Kusuma School of Biological Sciences,
> > Indian Institute of Technology Delhi,
> > New Delhi-110016,
> > India.
> >
> > Alternate E-mail : subhomoi at yahoo.com
> >
> > https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ
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