Hi, On Thu, Jun 1, 2017 at 3:35 PM RAHUL SURESH <drrahulsur...@gmail.com> wrote:
> I have few doubts in MD analysis. > > *How to calculate the deviation angle between two helix of a protein? (for > every ns) or in other words how can I know whether the two helices > (consecutive) > have moved apart during simulation? > Various of the analysis tools may be helpful here. Start at http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#commands-by-topic > *In saltbridge analysis how can I eliminate CL and NA ions? (Before the > analysis) > Probably through use of suitable index groups, which you probably learned about in tutorials or have seen in the documentation. Mark > PS:- Its Protein-Ligand complex simulated for 100ns. > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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. > -- 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.