Dear Dr. Case and the AMBER community,
I've just found how to compile nmode so as to be able to increase
nonbond cutoff to 99.0. I had to increase integer memory to cca.
10MWords (for a 3000-atom protein).
I assume now that the convergence problem was due to both, imposing
non-bonded cutoff and re-creating pairlist. Now I hope to succeed just
by using conjug grad mini and normal modes.
Thank you very much for your help.
Regards,
Martin Lepsik
David A. Case wrote:
>On Tue, Feb 10, 2004, ML wrote:
>
>
>
>>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)
>>
>>
>
>Set your cutoff to 9999. This will make the minimization converge
>more smoothly, and will remove any effect of changing cutoffs.
>
>I generally find that conjugate gradient minimization is fine...no need
>for Newton-Raphson. Just be patient (i.e. run lots of cycles of
>minimization).
>
>...good luck...dac
>
>
>
--
-----------
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
e-mail:lepsik.uochb.cas.cz
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Received on Wed Feb 11 2004 - 08:53:00 PST
