Thanks for your reply, Yes, you are correct, I want calculate the non-bonded interaction energies terms for Protein-Protein and Protein-Solvent system using rerun of the trajectory from a already finished simulation (using PME method).Please suggest whether there is any way to get these terms.
On Mon, May 23, 2011 at 23:06, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bipin singh wrote: >> >> Thanks for your reply, >> I have already done with the final simulation, and now if I have to >> change the method for electrostatic calculation(instead of PME) >> for energy group exclusion, then will it make sense i.e. how >> consistent it would be with my simulation results(with PME). >> Please suggest...... >> > > I'm not 100% clear on what you're doing, but I assume you're trying to do > some rerun of a trajectory to calculate various energy components? If > that's the case, there is a wealth of discussion on this topic in the list > archive. It is generally an exercise in futility or ambiguity. If a > trajectory was generated using long-range methods like PME, what sense is it > to re-calculate some component of the the energies of configurations that > were created using a different method? The long-range terms may have a > significant impact on the dynamical behavior, which you're now ignoring. > > If this is not your intent, then please explain further. > > -Justin > >> On Mon, May 23, 2011 at 21:28, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> bipin singh wrote: >>>> >>>> Hello users, >>>> I am getting the following warning during the grompp >>>> >>>> >>>> --------------------------------------------------------------------------------- >>>> WARNING 1 [file md.mdp]: >>>> Can not exclude the lattice Coulomb energy between energy groups >>>> >>>> >>>> ----------------------------------------------------------------------------------- >>>> >>>> I am providing the following energy groups and energy exclusion group >>>> in my mdp file >>>> energygrps=Protein SOL >>>> energygrp_excl=Protein Protein SOL SOL >>>> >>>> Please suggest me, why I am getting the above error and how to get rid >>>> of this error. >>>> >>> Presumably you're using PME for long-range electrostatics. The message >>> you're getting is grompp trying to help you realize that with PME it is >>> not >>> possible to completely exclude all energetic terms, since the long-range >>> mesh is always calculated. Only short-range nonbonded interactions (LJ >>> and >>> Coulombic terms) are excluded in the mechanism above. >>> >>> -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 >>> >> >> >> > > -- > ======================================== > > 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 > -- ----------------------- Regards, Bipin Singh -- 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
