[gmx-users] Forcefield parameters
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 28 08:57:08 CEST 2010
On 28/10/2010 3:03 AM, Sai Pooja wrote:
> Hi Mark,
> I am familiar with the section, however, I have a few doubts.
> When you say ...
> So modified protein-water VDW interactions can be introduced by
> defining all relevant "protein atom"-"TIP3P oxygen" [nonbond_params]
> terms.
> Do you mean that I can introduce [pairtypes] specifying interactions
> of all "relevant protein atoms" with "tip3p atoms"?
No, [pairtypes] are not relevant.
> and I do not understand - It may be simpler to modify the [atomtypes]
> to generate the "modified" VDW from the combination rule
> Would this not alter all non-bonded interactions for the atomtypes
> defined? I think I haven't understood thsi properly...
I was thinking of a flawed procedure. Ignore this part.
Mark
> Pooja
>
> On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>> wrote:
>
> I think manual 5.3.3 covers the relevant points. Let me know what
> is not clear.
>
> Mark
>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
> Date: Wednesday, October 27, 2010 9:41
> Subject: Re: [gmx-users] Forcefield parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
> >
> >
> > On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham
> <mark.abraham at anu.edu.au> wrote:
>
> >
> >
> > ----- Original Message -----
> > From: Sai Pooja <saipooja at gmail.com>
> > Date: Wednesday, October 27, 2010 8:52
> > Subject: Re: [gmx-users] Forcefield parameters
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >
> > > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul
> <jalemkul at vt.edu> wrote:
>
> > >
> > >
> > > Sai Pooja wrote:
>
> > >
> > >
> > > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at 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
> > --
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