Hi,
I would not do this. I would run my simulation as normal (no position restraints), and center my amino acid in post processing (gmx trjconv -pbc mol -center ...). You may need to make an appropriate index file. Alternatively you may want to use -fit instead of -center, but that's a matter of taste. Peter On 29-05-17 08:16, Saumyak Mukherjee wrote: > Hi Dilip, > > To fix the amino acid at the centre of the box first you have to use -c > flag with editconf. Later, during simulation you have to use > define=-dposres in the mdp file. This will include the position restrain > defined in the posre.itp file generated during the use of pdb2gmx. > > Best, > Saumyak > > On 29 May 2017 at 10:59, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > >> Hello, >> I have ran a md simulation of a amino-acid with solvent mixture. Now i view >> the trajectory in vmd and see tht the amino-acid moves sometimes toward the >> edge of the box,sometimes towards the corners and so on... >> Now how can i centre only the amino-acid to the centre of the box and rest >> (ie.,solvent mixture) to move as it is..ie., if i view the trajectory in >> vmd i want to fix only the amino-acid to be in centre,whereas the solvent >> mixtures to move around during the trajectory... >> How can i do this,...?? >> >> Thank you... >> >> -- >> 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> >> -- >> 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-requ...@gromacs.org. >> > >
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