On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/21/12 9:36 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I got confused about reading free energy difference from PMF curve. >> It is the difference between maximum value on PMF curve (plateau - >> final state) and the starting point corresponding to minima. >> >> So e.g. my curve starts at 0 [kcal/mol] going staright to minima of -2 >> kcal/mol and then increase obtaining plateau of 14 kcal/mol. DeltaG = >> -16 kcal/mol or -12 kcal/mol ? >> > > It seems that your system has discovered a more energetically favorable > location where the minimum is at -2 kcal/mol. It should not be assumed that > whatever arbitrary "start" point we choose is the energy minimum. In your > case, it is not. DeltaG is the difference between final and initial states. > Only you know what these states are. > > -Justin
Thank you. Ok - mu curve starts at 0 kcal/mol corresponding to the reaction coordinate of 0.5 nm. going to -2 kcal mol at 0.6 nm then increasing as I said before to plateau of 14 kcal/mol. My first window (shown by grompp) corresponds to 0.8 nm of the reaction coordinate... So the initial state should be at 0.8 nm which corresponds to 0.5 kcal/mol or always take the initial state as initial of the curve? Sorry, got confused. Steven > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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
