Re: Minimisation Protocol

From: Axel Kohlmeyer (
Date: Fri Oct 02 2009 - 12:24:56 CDT

On Fri, 2009-10-02 at 17:36 +0100, Philip Peartree wrote:
> Hi,

hi philip,

> I'm interested in what people do for pre-MD minimisation, e.g., do
> people fix any atoms, constrain any atoms, how many steps do people
> do? I have previously run about 10000 steps of unrestrained
> minimisation.

there is no general answer to your question other than: it depends.
it depends on the quality of the starting structure, how you
generated missing parts, how you prepare the total system, how
many components it has, how "fragile" your system is, how your
results are affected by artifacts from combining multiple pieces.
how good your parameterization is, and so on.

from demanding and complicated systems, you may need a very
complicated procedure, for trivial systems (e.g. the ones used
in the NAMD tutorials), you can get away with being fairly sloppy.


> This is on a enzyme in a water box, approx 50000 atoms.
> Thanks
> Philip Peartree
> University of Manchester

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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