[gmx-users] Forcefield parameters

[Justin A. Lemkul]

Sai Pooja wrote:
> On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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.
>  

Any change you might make to the TIP3P parameters (LJ parameters or charges) 
will inherently change the intermolecular interactions between whatever species 
are in your system.

-Justin

> -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/> <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 <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

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