[gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

[Faulkner, Matthew]

Thank you, I will try that. 

Matthew.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Dries Van Rompaey [dries.vanrompaey at gmail.com]
Sent: 13 April 2016 14:55
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

Hi,

You can do this using built-in gromacs tools. You want to make a suitable
index group using gmx make_ndx, after which you can use gmx distance to
measure the distance between your groups.

Dries
On 13 Apr 2016 3:50 p.m., "Faulkner, Matthew" <M.Faulkner at liverpool.ac.uk>
wrote:

> Hi all,
>
> Does anybody have a script, or reference where this has been done, for
> measuring distances between two residues in each time step of a simulation
> and exporting this data into a handy format like a text or csv file?
>
> I want to measure the distances over time between the nearest atoms of
> some residues that appear to have a conformation change but at the moment I
> only know how to do this manually.
>
> Regards,
> Matthew Faulkner.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.