----- 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
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