[gmx-users] Forcefield parameters

[Sai Pooja]

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.
>

In that case, changing sigma and epsilon of tip3p water molecules in the
ffnonbonded.itp files will change both water-protein and water-water Vdw
interactions.
Also if I multiply q for tip3p water molecules in the same file, I can
modify the water-water and water-coulomb interactions.

-Pooja

> -Justin
>
>  Pooja
>>
>>
>>
>>    Yes.
>>
>>    -Justin
>>
>>
>>        Pooja
>>
>>        --         Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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