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

[Peter Kroon]

Keep discussions on the list. I am not your personal help. I will not
respond to future e-mails to my personal address.


Type `gmx trjconv -h` and read.

Also read
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


On 29-05-17 13:43, Dilip H N wrote:
> Thank you...
> nw the amino-acid is placed in the middle, but i have two solvents as
> mixture (solvent A,B).
> But the problem is tht nw the amino-acid remains in the centre but the
> solvent B is moving out of the box....
> How can i solve this issue..??
>
> Thank you...
>
> On Mon, May 29, 2017 at 4:10 PM, Peter Kroon <p.c.kroon at rug.nl
> <mailto:p.c.kroon at rug.nl>> wrote:
>
>     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.
>
>     Peter
>
>
>     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,
>     >
>     > DILIP.H.N
>     > Ph.D Student
>     >
>     >
>     >
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>     >
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>     >
>
>
>
>
>
> -- 
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student