[gmx-users] Forcefield parameters

[Sai Pooja]

On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <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?

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 | (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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