[gmx-users] center

[Tsjerk Wassenaar]

Hi Malihe,

Check the suggested trjconv workflow at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk

On Sun, Dec 6, 2015 at 12:39 PM, Malihe Hasanzadeh <ml.hasanzadeh at gmail.com>
wrote:

> Hi
> I have run a ligand-protein MD simulation for 50 ns by gromacs 5.0.5. At
> the end of simulations, molecule is out of the box.I have used from two
> below command for center but neither of them isn't work and molecule still
> is out of box.
>
> trjconv -f md300.trr -o md300t.xtc -fit rot+trans -s md300.tpr
> trjconv -f md300.trr -o md300t.xtc -pbc mol -center -s md300.tpr
>
> So how to center the molecule before going for analysis?
> Thanks
> --
> 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.