[gmx-users] Forcefield parameters

[Sai Pooja]

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"?


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...


Pooja


On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <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>
>  Date: Wednesday, October 27, 2010 9:41
> Subject: Re: [gmx-users] Forcefield parameters
> To: Discussion list for GROMACS users <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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> >
> >
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