On 12/07/10, nishap.pa...@utoronto.ca wrote: > Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > > I actually want to plot my simulation with ad without the attractive term C6 > of van der Waals and superimpose them to see the difference. >
g_sigeps -c6 0 probably does that. See g_sigeps -h Mark > > > > > > >nishap.pa...@utoronto.ca wrote: > >>Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > >> > >> How does sigeps read the input file? I tried using sigeps to plot LJ for > >> different solutes in solvent and it gives me the same C6 and C12 value, > >> when it runs, which seems a weird. > >> > >>c6 = 1.00000e-03, c12 = 1.00000e-06 > >>sigma = 0.00000, epsilon = 0.00000 > >>Van der Waals minimum at 0, V = nan > > > >g_sigeps does not take any input file. It produces an LJ curve based > >on command line parameters. I guess this is not what you are after, > >although that's exactly what it sounded like from your last post. > >Perhaps you need to re-phrase your question. If you just want to plot > >van der Waals energy terms, use g_energy to pull them out of the .edr > >file. > > > >-Justin > > > >> > >>Is it the default? > >>> > >>> > >>>nishap.pa...@utoronto.ca wrote: > >>>>Hello, > >>>> > >>>> Is there an option to plot Lennard Jones potential? I tried looking > >>>> through the list and manual but I did not find any suggestions on how > >>>> I could plot a LJ 6-12 potential plot. > >>>> > >>> > >>>g_sigeps > >>> > >>>-Justin > >>> > >>>>Nisha > >>>> > >>>> > >>> > >>>-- > >>>======================================== > >>> > >>>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 > >> > >> > >> > >> > > > >-- > >======================================== > > > >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 thewww interface or > send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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