AMBER Archive (2004)

Subject: AMBER: Nmode convergence

From: ML (
Date: Tue Feb 10 2004 - 01:36:27 CST

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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