AMBER Archive (2004)

Subject: Re: AMBER: Nmode convergence

From: ML (
Date: Tue Feb 10 2004 - 09:26:12 CST

I suggest myself a solution; run minimization several times (possibly
only conjug.grad.) until the "dependence" on pairlist goes down. Then,
one round of Newt-Raphs mini (will it still be necessary?), write out
pairlist and read in pairlist for normal modes calcul.

Any suggestions or comments?


Martin Lepsik

ML wrote:

> Dear AMBER team,
> I minimize a 3000-atom protein with Newton-Raphson (after conjugate
> grad.) as I want to calculate normal modes. I use convergence
> criterion of E10-4 or 5E10-5 but for the normals modes it's much
> higher (E10-3 to 5E10-4). I understand that this has to do with
> re-creating the pairlist when restarting but how to proceed? (the same
> thing happened after conj.grad. mini)
> What (highest) gradients are recommended for both parts of
> calculations? Is there a way how to keep down the difference in
> gradients between Newt-Raph and nmodes? Are there some tricks in
> keywords or compilation? (I use double-precision, no DISTAR and
> unformatted restarts)
> Thanks in advance for your answers.
> Best regards,
> Martin Lepsik

Martin Lepsik
Dept. of Molecular Modeling
Institute of Organic Chemistry & Biochemistry
Czech Academy of Sciences
phone: +420-220 183 540
fax:+420-220 183 292

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