HI Renato generally I have always used a combination of SD and CG methods for minimization switching after ncyc=2500 or maybe 3000.
It has worked for all the 10-12 proteins I have worked on setting up MD simulations.
Thanks
Debarati
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From: Renato Araujo<mailto:renatoacufpa.gmail.com>
Sent: 23 June 2020 21:52
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Minimization erro
Dear David
On here
Do just enough minimization to get rid of really bad
initial forces, then spend your computer time on MD, gradually releasing
the restraints.
You suggest me to which minimization?
Thanks in advance for the suggestions
Em ter., 23 de jun. de 2020 ąs 22:02, David A Case <david.case.rutgers.edu>
escreveu:
> On Tue, Jun 23, 2020, Renato Araujo wrote:
> >
> >I'm doing four minimization steps as follows:
> >In the first, you specify the water and ion residues (cl- or Na +).
> >In the second, only the protein residues (H minimization);
> >In the third, it specifies protein + water (Leaving ions out).
> >The last is a general minimization, I don't specify anything.
> >
> >The first three steps occur without errors, but the last one gives this
> >messages in the terminal:
>
> In addition to what Debarati DasGupta suggested, try running a (short)
> serial job. But I'm guessing that you are seeing failures arising from
> hydrogen atoms getting too close to other atoms, since you have very
> large negative electrostatic energies.
>
> The only safe way to run things is either to use SHAKE (which is what
> most people do, if they are planning to use the minimization as a
> starting point for subsequent MD); or use the "lmod" action in parmed to
> get rid of hydrogens in zero vdW radii.
>
> As an aside, if you *are* just minimizing to get ready for MD, you are
> probably doing way more minimization (and more complex minimization)
> than is necessary. Do just enough minimization to get rid of really bad
> initial forces, then spend your computer time on MD, gradually releasing
> the restraints.
>
> ....dac
>
>
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--
Prof Dr Renato Costa
Instituto Federal do Parį - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Wed Jun 24 2020 - 06:00:11 PDT
