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 > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> >
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