Debarati
Thank you
Your suggestions and information are being valuable.
Att.,
Em qua., 24 de jun. de 2020 às 09:44, Debarati DasGupta <
debarati_dasgupta.hotmail.com> escreveu:
> 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
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> 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 às 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 Pará - IFPA
> Grupo de Modelagem Molecular - UFPA
> Tel.+55 91 985484622
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--
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Wed Jun 24 2020 - 06:30:04 PDT
