I think manual 5.3.3 covers the relevant points. Let me know what is not clear.
Mark ----- Original Message ----- From: Sai Pooja <saipo...@gmail.com> Date: Wednesday, October 27, 2010 9:41 Subject: Re: [gmx-users] Forcefield parameters To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > 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. > -- > 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
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