With all due respect, this is clearly a RT*M moment. * = F
Joao Henriques On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Monisha Hajra wrote: > >> Hi Justin, >> >> I am trying to follow the protocol only. >> More than the Gromacs own website, I find >> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is >> more useful. >> >> > Clearly. This is one of many tutorials linked from the site I posted > before. > > However, I am stuck at one step which is mentioned : >> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html >> >> I am not able to understand how to create traj.trr, traj.xtc and ener.edr >> file. Remaining all is self explained in the previous link. >> >> > These files are output by mdrun, i.e. actually running a simulation. > > -Justin > > Really appreciate any help. >> >> Regards >> Monisha >> >> >> On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Monisha Hajra wrote: >> >> Hi User, >> >> I have a protein which I have modeled by Homology modelling. The >> modeled protein has no water molecules in its surrounding >> environment. >> >> How should I add water molecule so that I can start the >> simulation process? >> >> >> Please refer to the abundant tutorial material on the website: >> >> http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use >> >> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation >> >> -Justin >> >> Regards >> Monisha >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists