[gmx-users] langevin dynamics

[David Mobley]

Just my unasked-for two cents: Langevin dynamics in water is probably
a poor substitute for some representation of water. Langevin can
provide some of the friction/noise of water -- but electrostatics
interactions are very different in water than in vacuum. Langevin
dynamics is probably not a substitute for an implicit solvent model.

On 10/30/07, Syma Khalid <syma.khalid at bioch.ox.ac.uk> wrote:
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> Dear all,
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> I was wondering if someone could offer some advice?
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> I would like to run an atomistic langevin dynamics simulation (as I don't
> want to include water explicitly). If I add the appropriate langevin
> dynamics options in the mdp file, then is there any reason why I shouldn't
> use explicit counter ions (unfortunately my protein has an overall charge)?
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> Obviously I would use periodic boundary conditions so the ions don't wander
> off.
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> Many thanks in advance for your suggestions/comments,
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> -Syma
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> ***********************************************************************
>  Dr Syma Khalid
>  RCUK Fellow (Chemical Biology)
>  School of Chemistry
>  University of Southampton
>  Highfield
>  Southampton      phone: (0)2380-594176
>  SO17 1BJ          email: S.Khalid at soton.ac.uk
>  U.K.
> ***********************************************************************
>
>
>
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