Hi Surya, I'm not sure I understand what you want to do. Do you want to energy minimise an entire trajectory? After the production phase? Why?
The -c flag in mdrun is the output, the last conformation sampled during the mdrun. You can use this output file as the input structure for an energy minimisation (-c option in grompp to prepare the .tpr file), I just don't see the point in doing that. Also, -c flag in grompp doesn't accept .xtc files. If you type "grompp -h" you'll see that. Cheers, On 28 September 2016 at 05:53, Seera Suryanarayana <paluso...@gmail.com> wrote: > Dear gromacs users, > I have done simulations for 100ns. I would like to do energy minimization > by using trajectory file which I got after production phase. Can I do > energy minimization passing the trajectory file to -c argument? If it is > yes, then tell me how to do it. > > Thanks in advance > > Surya > Graduate student > India. > -- > 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. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- Catarina A. Carvalheda PhD Student Computational Biology Division SLS & SSE University of Dundee DD1 5EH, Dundee, Scotland, UK -- 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.
