Re: [AMBER] different number of waters

From: David A Case <>
Date: Wed, 18 Jun 2014 08:49:05 -0600

On Wed, Jun 18, 2014, newamber list wrote:
> But I would like to know how AMBER differs
> in adding waters compared to Gromacs as a initial guess

I don't know what Gromacs does. Amber deliberately makes the box a little too
big (and the initial density too low), in order to avoid bad contacts in the
intial structure. I'm not defending this as optimal; it's really just an
historical artefact. But so far, no one has thought it important to fix this.
If Gromacs does a better job, that is fine.


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Received on Wed Jun 18 2014 - 08:00:03 PDT
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