On 11/4/13 8:55 AM, kiana moghaddam wrote:
Dear Justin
It is obvious that emtol value can not be zero or negative. but you wrote in
your email " For more sensitive calculations like free energy simulations and
normal modes, you will want to minimize much more thoroughly (for NM, emtol <
1) and in double precision". what did you mean by saying emtol<1? Anyway, my
I mean exactly what I said. You should set emtol to some value of 1 or less as
a target for NMA.
question was: for free energy calculation in double precision, what should be
the best value for emtol?
I have not worked with systems that have required such strenuous minimization,
but I believe the general recommendation (if necessary for whatever you're
working with, and I'm not prepared to try to guess about what you're doing) is
to minimize as far as you possibly can. Set some very low value of emtol and
some very high value of nsteps and let the EM algorithms churn away. You will
usually need several rounds of EM using different methods to achieve this.
Published literature and previous posts to this list (in the archive) should be
sufficient to guide you.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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