Thank you justin, I read the articles, archive and also g_sham -h,
As I mentioned in previous mail, I simulated four random coil peptide , they started to form Beta sheet structure after 20 ns ..( simulation time 100ns ) My interest is how to draw the Free energy diagram for Potential energy and Structures...(eg. RMSD, Gyrate, different cluster , with different structure at particular time ) . Would you please tell me how to do it in gromacs with command line and needed input. I tried it a lot but not able to find the way .. I will be a very grateful to you for ur help .. With best Regards Rama david. On Thu, Apr 4, 2013 at 1:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/4/13 2:14 AM, rama david wrote: > >> Dear Friends, >> I simulated the 4 peptide in water box . >> As they come close to each other they start to from anti-parallel >> beta sheet structure. >> >> >> >> Now I want to draw the Free energy surface for the >> same ..How is there pot energy ??? >> >> Would you please tell me how to do it .. >> >> ( I read about g_sham -h, I tried it, but not understand properly) >> >> I will be very grateful for your suggestion and help.. >> >> > The logic behind g_sham was just posted to this list no more than a few > days ago. > > http://lists.gromacs.org/**pipermail/gmx-users/2013-**March/079810.html<http://lists.gromacs.org/pipermail/gmx-users/2013-March/079810.html> > > It calculates a free energy surface as a function of two variables of your > choosing. As David noted (http://lists.gromacs.org/** > pipermail/gmx-users/2013-**March/079813.html<http://lists.gromacs.org/pipermail/gmx-users/2013-March/079813.html>), > the result may not correspond to a true quantitative representation of free > energy differences, though. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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