[gmx-users] Calculating avergae structure from the simulation

[Chandan Choudhury]

gmx rmsf -f *.xtc -s *.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq
bfactors.pdb -res

This would give you a average structure.

On Wed, Jun 8, 2016 at 5:21 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> I had run an unrestrained 50 ns simulation of a protein-ligand complex
> using GROMACS to check the stability of the force field used and compare
> with previous literaure.
>
> Then I dumped the strucuture from the last frame of the 50 ns simulation
> and used it for pulling and umbrella sampling simulations.
>
> Now, the reviewer is asking me this "Reference structure should have been
> the average structure, not the final state seen at the end of 50 ns MD run.
> "
>
> Is there any tool in GROMACS by which I can calculate the average structure
> ?? I was thinking that this is a normal procedure to conduct the
> simulations.But now I am confused. Kindly comment.
>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
> --
> 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.
>



-- 

Chandan Kumar Choudhury
Post Doctoral Fellow
Clemson University
South Carolina
USA

*"All work and no play makes Jack a dull boy...”*