[gmx-users] Chain length of a polymer

[Alessandra Villa]

Hi,

I  understood, that you would like to monitor the distance between the two
ends of your chains along the simulation. If this is the  case
 you could use
gmx distance (see
http://manual.gromacs.org/current/onlinehelp/gmx-distance.html) together
with the appropriate selection (e.i. you could calculate the distance
between the com of the two polymer ends)
In alternative you can use gmx mindist (
http://manual.gromacs.org/2019/onlinehelp/gmx-mindist.html)

To generate index files you can use gmx make_ndx (
http://manual.gromacs.org/2019/onlinehelp/gmx-make_ndx.html)

Best regards
Alessandra

On Thu, Nov 21, 2019 at 1:40 AM Shan Jayasinghe <
shanjayasinghe2011 at gmail.com> wrote:

> Dear Gromacs Users,
>
> I have a polymer molecule in my MD simulation and I want to calculate how
> chain length varies with simulation time. How can I do that with Gromacs
> software? Can I use gmx distance? Do I need to create a group with backbone
> atoms of the polymer chain in the index file for the calculation?
> Appreciate your help.
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
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