Sai Pooja wrote:
On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
========================================
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