On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Sai Pooja wrote: > > >> >> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Hi, >> I want to change the non-bonded parameters to modify the >> interaction between water molecules and protein molecules. >> I am using CHARMM forcefield with Tip3p water. >> The ffnonbonded.itp file of the forcefield has non-bonded >> parameters for tip3p water. Can I achieve the above by changing >> these parameters? >> >> >> That depends on your definition of "modify," but yes, in a way, you >> can make changes here. >> 1) Modify - Multiply sigma and epsilon by a constant >> >> If yes, will this also change the non-bonded parameters for >> water - water interaction? >> >> 2) Is there a way to add a new ifdef perhaps such that a modified sigma >> and epsilon can be used for water-protein interactions and the unmodified >> parameters can be used for water-water interactions? >> >> > > Nonbonded interactions are calculated during the simulation by applying the > combination rules defined by the force field. There is no simple way to do > this with an ifdef, since that is just in the topology. You can't > conditionally apply nonbonded parameters. That just sounds like a recipe > for breaking a force field. > In that case, changing sigma and epsilon of tip3p water molecules in the ffnonbonded.itp files will change both water-protein and water-water Vdw interactions. Also if I multiply q for tip3p water molecules in the same file, I can modify the water-water and water-coulomb interactions. -Pooja > -Justin > > Pooja >> >> >> >> Yes. >> >> -Justin >> >> >> Pooja >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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