On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 6/28/12 6:33 AM, Steven Neumann wrote: >> >> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: >>> >>> Dear Steven, >>> >>> Where are you working? >> >> >> I work in UK, London. Why are you asking? >> >> >>> >From my experience the g_energy -fee only gives a free enrgy estimate >>> for the whole system, so one has to pull out all the energy terms based on >>> your index file of interest and sum them in a spread sheet. if the -fee can >>> do the energy estimates for a specific set, please let me know this would be >>> valuable to me. >> >> >> I think I will just need a potential energy between those residues (LR >> and Coulombic) and then can get the effective potential >> Ueff=-kTln<e(-BU) >> and then g_dist. >> > > If you are using PME, there is no trivial way to decompose the reciprocal > space term. > > -Justin
But if I will get the effective potential with respect to the distance I can adjust non bonded parameters to this curve in coarse grained model. Am I right? > > -- > ======================================== > > 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