On Mon, Aug 23, 2010, George Tzotzos wrote:
>
> Is there a rule of thumb as to what weight to apply for energy
> minimisation? How high should be the restraint_wt be set?
Carlos' answer, or just trying your own experiments, is probably best, since
we don't know what system you have, etc.
My rule of thumb, however, is this: A weight of 5 is "strong", and will
keep the structure within a few tenths of angstrom from the starting point
(unless you have bad contacts in the initial structure that absolutely need to
be fixed.)
I usually start MD as soon as I can (for most projects), since that will
perform both equilibration and bad-contact removal. I think of a weight of
0.1 as "weak", and often use that for much of the equilibration period.
But there is no universal protocol, and no substitute for trying different
ideas on your particular system.
....dac
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Received on Mon Aug 23 2010 - 05:30:05 PDT
