[gmx-users] Regarding centering the molecule/protein during Simulation

Peter Kroon p.c.kroon at rug.nl
Mon May 29 12:40:50 CEST 2017

Keep discussions on the list.

As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
...`. In your example this would be:

> gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*

> vmd  mdx.xtc

If you can't figure it out from here, try `gmx trjconv -h` and read.


On 29-05-17 12:16, Dilip H N wrote:
> Thank you for reply..
> I have ran energy minimization,followed by nvt, followed by md run.
> In this md run mdp (md.mdp),
> nw after the simulation ends, i can view the trajectory by giving
> command as :-
>  gmx trjconv -f md.xtc -s md.tpr -pbc mol -o mdx.trr/xtc/gro
> and nw if i view the mdx.trr/xtc/gro in the vmd as :-
>  vmd  mdx.trr/xtc/gro 
> will the amino-acid only be at the centre while viewing it throught
> the trajectory and moving solvent molecules around as usual..??
> Or can u kindly help me which r the exact commands tht i need to give
> in order tht while viewing the full trajectory in vmd only the
> amino-acid should be in centre , whereas the solvent molecules should
> move around as usual..
> -- 
> With Best Regards,
> Ph.D Student
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>

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