On Thu, Jan 20, 2011 at 6:36 PM, Marc-André Dubois
<ma.dubois.umontreal.ca>wrote:
> Jason,
> Thank you very much for your reply. I will try to break the
> organic molecule as you suggest. I don't why however SQM seems to take a lot
> of time comparing with MOPAC..
>
This has been discussed a couple times in the past on this list, I believe.
I think it has to do with different tolerance criteria for, i.e., SCF
convergence. I believe that SQM is a little more stringent which means that
it must solve more SCF iterations than mopac is doing. I think you'll get
similar timings if you manually adjust these settings so they're consistent
across both programs.
Hope this helps,
Jason
>
> Le 2011-01-20 à 18:26, Jason Swails a écrit :
>
> > Hello,
> >
> >
> > On Thu, Jan 20, 2011 at 5:47 PM, Marc-André Dubois
> > <ma.dubois.umontreal.ca>wrote:
> >
> >> Hi,
> >> I just started using AmberTools 1.4 and I am now able to successfully
> >> achieve some tutorials present on http://ambermd.org/tutorials/. I try
> to
> >> repeat an exercise very similar to the B4 tutorial, but have some
> >> difficulties to complete the process. First, I am not able to run mopac
> with
> >> antechamber. I almost tried adding mopac.sh, but it is not functional.
> So I
> >> tried to run antechamber with sqm to get the charges, but I get a
> >> "segmentation Fault". My main concern is about the number of atoms of my
> >> organic molecule. The compound is a Trimer with a total of 230 atoms. Is
> >> there a limit in ambertools regarding the number of atoms? I also tried
> to
> >> calculate the charges
> >
> >
> > 200 atoms is a large system to treat with quantum mechanics. One reason
> you
> > may have gotten a segfault with sqm is because your system doesn't have
> > enough memory to allocate to the job. In any case, this seems to be a
> very
> > difficult case for antechamber/sqm to handle. Perhaps you can break the
> > organic molecule down into individual "residues" (much like a protein is
> > broken down into amino acids) and parameterize each of those separately.
> >
> >
> >> using my own version of mopac, using mainly babel to convert my file in
> a
> >> mol2 file, but I still face a problem in the molecular dynamics. The
> >> movements seems erratic. Am I the first to face this situation? Thanks,
> >>
> >
> > This is not terribly helpful. "Erratic" could mean many things. It
> could
> > be that you're just talking about periodic COM translation removal (to
> > eliminate drift). You should do some kind of RMS fit before really
> looking
> > at the dynamics so you know that translations and rotations aren't making
> it
> > 'appear' worse than it is.
> >
> > Also note that charge derivation is only one step of force field
> creation.
> > You also need to make sure that you have the bond, angle, and (most
> > difficultly) the dihedral parameters. Dihedral parameters are the
> hardest
> > to get *right* since they're a correction term that are often
> misunderstood
> > (and you have the 1-4 scaling that complicates issues).
> >
> > Hope this helps (a sqm/antechamber expert may interject here with more
> > helpful advice),
> > Jason
> >
> >
> >> Marc-André Dubois
> >> Université de Montréal
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 20 2011 - 16:00:11 PST
