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).
Brian
On Wed, Jun 18, 2014 at 10:49 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Wed Jun 18 2014 - 08:30:02 PDT
