Sai Pooja wrote:
On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Sai Pooja wrote:
On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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.
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
========================================
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