AMBER Archive (2003)

Subject: Re: How to do a rigid solvent model?

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 04 2003 - 12:16:51 CDT

On Fri, Jul 04, 2003, Marco Aurelio Correia Preto wrote:
>
> We are doing some molecular dynamic runs of small non-standart peptides (in
> water) and we would like to do the smae dynamics in other solvents! There
> are a couple of potential for organic solvents, but some of them are rigid
> one! How can we do this in Amber (version 6 is the one we have)? Can we use
> very large force constants to force a rigid conformation?
>

It is more typical to use SHAKE to keep solvent molecules rigid. Some other
solvents (chloroform, methanol, acetonitrile, ...) are available at:

     http://pharmacy.man.ac.uk/amber/

..good luck...dac
    

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David A. Case                     |  e-mail:      case_at_scripps.edu
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