Hi Justin (and gmx-users), I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape?? Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham.
What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results? I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing! Natalie ------------------------------------------------ Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 ------------------------------------------------ ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: > I was recently told in passing that it would be possible to construct a > 'potential energy landscape' from the simulations I have performed. > This way I could remove any loading rate differences between simulations > and experimental force experiments I've been performing ... however I > cannot find anywhere in which this is mentioned. > > The only thing close I could find that was close was the free energy > landscape using g_anaeig under the Dihedral PCA > (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca > <http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca>) > however, I'm not sure this is what I'm looking for. > > Does anyone know where I would be able to find out / read more about how > to create potential energy landscapes from my simulation outputs? > g_sham produces free energy landscapes for any variables plotted against one another. -Justin -- ======================================== 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