Re: AMBER: Molecular dynamic issues

From: Carlos Simmerling <>
Date: Tue, 23 Jan 2007 09:54:24 -0500

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* <
> <>> 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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Received on Wed Jan 24 2007 - 06:07:38 PST
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