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. > -- ================================ *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com smukher...@sscu.iisc.ernet.in ================================ -- 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.
