Re: Can I use another solvent rather than TI3P model in namd for MD simulations ?

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 29 2009 - 08:32:30 CDT

On Sun, 2009-06-28 at 11:30 +0800, Wang Yf wrote:
> Hello all,

hello,

> Can I use another solvent rather than TI3P model in namd for MD
> simulations ? If I can ,how do I make it, could anyone give me

please be more accurate.

do you mean some other water potential
or some completely different solvent?

there is no technical limitation to the method
to use a different solvent or a different water
potential, but you have to keep in mind that
will basically need a complete new force field
that has been parametrized with the new solvent.

existing force fields that NAMD can handle all
contain _effective_ pairwise potentials that
include solvation effects. using those parameters
with a different solvent will break the balance
between the solvent-solvent and solvent-solute
interactions. so you have to take this into account
when using a different solvent.

cheers,
   axel.

> advice ? Thank you in advance.
> Best wishes!
> Wang Yf
>
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> ______________________________________________________________________
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-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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