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.abra...@anu.edu.au
<mailto:mark.abra...@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 <saipo...@gmail.com <mailto: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
<mailto: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
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