[gmx-users] Forcefield parameters

[Sai Pooja]

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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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