On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> > > ----- Original Message ----- > From: Sai Pooja <saipo...@gmail.com> > Date: Wednesday, October 27, 2010 8:52 > Subject: Re: [gmx-users] Forcefield parameters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > 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. >> > > Not quite right. Parameters for VDW are calculated from the combination > rules from the atom-specific values given in [atomtypes] only as a last > resort. [nonbond_params] are used in preference to such. > > So modified protein-water VDW interactions can be introduced by defining > all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms. It may be > simpler to modify the [atomtypes] to generate the "modified" VDW from the > combination rule, and introduce the "normal" TIP3P oxygen-oxygen interaction > via [nonbond_params]. > Mark, could you please elaborate the method? > > Mark > -- > 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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