AMBER Archive (2007)

Subject: Re: AMBER: Molecular dynamic issues

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Wed Jan 24 2007 - 08:41:19 CST

Thank you very much Carlos.

Sophie

Selon Carlos Simmerling <carlos_at_csb.sunysb.edu>:

> leaving explicit water in MD simulations with GB or other continuum solvents
> can be difficult. If the water is tightly bound to the solute, it may
> not be a
> problem. Surface waters might "exchange" with the bulk. Several groups
> have worked on hybrid explicit/implicit water models, you should read the
> literature on those to see the advantages and the challenges in using them.
> we recently reviewed these in the ACS Annual Report in Comp Chem
>
> *1. *Okur, A. and Simmerling, C., /“Hybrid Explicit/Implicit Solvation
> Methods”/, Annual Reports in Computational Chemistry, 2:97-109 (2006).
>
>
> Chupakhin Vladimir wrote:
>
> > I have the same question :)
> > What if we leave a water in GB model?
> > so we will have solution of the water.
> > Water with the additional Force-Field Restrains?
> > I am just guessing...
> > Vladimir
> >
> >> On 1/23/07, *Sophie Barbe* <sbarbe_at_insa-toulouse.fr
> > <mailto:sbarbe_at_insa-toulouse.fr>> wrote
> > > 2- Is it better to use a cubic or an octahedral box to simulate the
> > dynamic of a
> > > protein in solution?
> >
> >
>
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Chercheur Post-doctoral
Institut National des Sciences Appliquées
Groupe Ingénierie Enzymatique Moléculaire
Laboratoire Biotechnologie-Bioprocédés (UMR CNRS 5504/ INRA 792)
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