On 26 August 2011 15:17, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Juliette N. wrote: > > >> >> On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvcha...@gmail.com<mailto: >> vvcha...@gmail.com>> wrote: >> >> >>. Now it is clear that >> >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded >> potentials. Thank >> >> you so much. >> >> The answer actually depends on what you call "nonbonded potential". If >> you want to calculate e.g. the interaction energy between two >> molecules, then you should NOT include this term. >> >> >> Thank you for you reply. I am actually interested in interaction energies >> (cohesive energy between particles which is related to enthalpy of >> vaporization) and noticed that inclusion of this term results in far less >> accurate results. The net energy is of repulsion type and adding a positive >> term ( LJ-1-4) makes my results inaccurate. I am already using nexcl = 3 in >> the topology which means 1-5, 1-6 neighbors are accounted for. But still LJ >> -1-4 is appearing. So far I have been ignoring this term (energy value) in >> my calculations, but my concern is that by just neglecting this energy term >> (value) I am not ignoring the actual effect of a potential term on the >> physics of the system. Is there any way to switch off this term? >> >> > The term arises because nrexcl is set to 3. You should not adjust this > value, as the force field was likely parameterized with this setting in mind > and 1-4 interactions are calculated and scaled very specifically for certain > reasons, not the least of which are dihedral interactions. > > Please keep in mind that (as I believe Mark recently said), you should not > necessarily expect biomolecular force fields, which were designed to > reproduce certain elements of protein dynamics (and sometimes other > molecules), to necessarily reproduce the properties of any other material or > other quantities. You may be finding simply a limitation of whatever force > field you've chosen; it may not be suited to your task and you may end up > having to design your own force field or modify an existing one. Though > that can be an entire Ph.D. in itself... >
Thank you Justin. I am using OPLSAA which is suited for hydrocarbons and my system contains only saturated hydrocarbon macromolecules. I hope I am using the appropriate FF. I keep nrexcl to its default value but I am wondering if I can consider LJ SR (or coulomb SR) as the only nonbondd terms since the quantity I am looking at is cohesion between molecules. LJ 1-4 is to do with non bonded but intra molecular interactions which does not affect the interaction energies. Am I making ad hoc changes to the force field in this way or I am allowed to look for the terms (LJ SR or coulomb SR) according to the definition of the quantity I am after? Thanks, >> >> >> -- >> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >> Univ. Rochester, Rochester, New York 14627-0216 >> THE UNITED STATES OF AMERICA >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> -- >> Thanks, >> J. N. >> >> > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N.
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