[gmx-users] Forcefield parameters

[Justin A. Lemkul]

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.

-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

========================================