Subject: PBC vs. cluster

From: Rodolphe Pollet <[email-masked]>
Date: Fri, 22 Mar 2002 16:04:03 +0100 (MET)

Hi everyone,

I am rather new in the field of classical Molecular Dynamics and i wonder what 
the pros and cons are between working on a very big cluster or choosing periodic 
boundary conditions. Don't you think there are some drawbacks in periodicity, 
especially if your potential is long-ranged ? Are big clusters really doomed 
because of Ewald correction or other tricks ? Are there any alternatives ?

Thanks,

Rodolphe Pollet.

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From: Konrad Hinsen <[email-masked]>
Date: 22 Mar 2002 17:20:13 +0100

Rodolphe Pollet <[email-masked]> writes:

> I am rather new in the field of classical Molecular Dynamics and i
> wonder what the pros and cons are between working on a very big
> cluster or choosing periodic boundary conditions. Don't you think

You don't say what kind of system you are working on. Basically you
must decide decide whether you are more worried by artificial
finite-size effects (e.g. surface tension) or by artificial
periodicity.
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From: Rick Venable <[email-masked]>
Date: Fri, 22 Mar 2002 11:35:50 -0500

On Fri, 22 Mar 2002, Rodolphe Pollet wrote:
> there are some drawbacks in periodicity, especially if your
> potential is long-ranged ? Are big clusters really doomed because of
> Ewald correction or other tricks ? Are there any alternatives ?

There can be consequences of representing a non-periodic systems such as
protein in aqueous solution with periodic boundary conditions, but there
are also consequences to using a stochastic air:water boundary for a
protein in a sphere of water as well.  In both cases, an adequate
thickness of solvent surrounding the solute is needed to reduce the
impact of the boundary treament.  In periodic systems, one can add ions
to the solution to help screen out the longer range electrostatic
effects, esp. when using Ewald methods.

Particle-Mesh Ewald methods scale reasonably well on Linux clusters with
CHARMM and AMBER, but as for most MD codes, a higher speed node
interconnect such as Myrinet may be essential to get usable scaling on
these types of clusters.  Ethernet scaling under the 2.4 Linux kernel is
particularly bad; the 2.2 kernel with the 'tcpfix' patch is highly
recommended clusters using TCP/IP over ethernet.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
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From: Richard Gillilan <[email-masked]>
Date: Fri, 22 Mar 2002 11:42:23 -0500

Back when I did simulation of reactions in
solution, we used truncated octahedral 
boundary conditions because these were
supposedly less likely to bias calculations
by introducing periodicity. Problem is
that PBC's can actually introduce a 
significant computational overhead since
they are called in the inner loops of the
code. 

I'm especially interested in how people
handle periodicity when they are
simulating crystallization and do not
want to bias the results by assuming a
certain unit cell.

Richard Gillilan
MacCHESS
Cornell University

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From: Michael Brunsteiner <[email-masked]>
Date: Fri, 22 Mar 2002 18:00:13 +0000

> want to bias the results by assuming a

didn't read it myself but i think what you want could be in:
BERNASCONI et al., JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS  
56 (3-4): 501-505 MAR-APR 1995

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Michael Brunsteiner
Centre for Theoretical and Computational Chemistry
University College London
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