Re: [AMBER] different number of waters

From: Brian Radak <>
Date: Wed, 18 Jun 2014 11:01:27 -0400

Maybe I'm misreading this situation, but it seems to me that users (of both
programs) are somehow expecting "a buffer of 15 angstroms" or whatever to
mean something specific and reproducible when in fact it is a vague
statement nearly devoid of meaning (unless you heavily describe the
protocol used).

I guess the bottom line is that nobody really expects a difference in a few
hundred or thousand waters to cause statistical (or even systematic) errors
in a simulation of a large system, as would be consistent with ensemble
equivalence. I'm sure there's a lower limit where this could/would matter,
but it would be, in my opinion, eminently foolish to run simulations
anywhere near that point for a variety of other reasons (which would
probably lead to even larger errors).


On Wed, Jun 18, 2014 at 10:49 AM, David A Case <>

> 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.
> ....dac
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> AMBER mailing list

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Received on Wed Jun 18 2014 - 08:30:02 PDT
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