Hi Gustavo:
Thanks.
As to your
"I just wanted to add here that, for a molecule this size, DIVCON is
probably one of the best possibilities, since it has been built
exactly with that in mind. I can't tell you much about parallelization
there, though."
from the web one learns about the existence of divcon 4.0, divcon 4.5, and
divcon lite. Probably it is the last one implemented in antechamber. My
divcon.out file indicates still another name "DIVCON 2005", which had been
compiled with HANS_LAPACK library. All other directives where not defined, in
particular "MPI_NOMC" and "MPI_IS_ON" were not defined, which seems to suggest
that divcon might be compiled parallel.
I also want to add that getting partial charges from another (may be parallel)
program could be possible. Then, however, assigning the charges for my molecule
would not be a trivial task, many many mistakes coming out from the tricking
stereochemistry, with so much overlapping in 3D. It was only thanks to VMD that
I could check (and correct heavily) the pdb file that was prepared with a MM
package. If not else, it would be so time consuming, and never sure to have
done correctly.
regards
francesco
--- Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> OK, I'm not an expert in antechamber, but I'll try some of the points here:
>
> > (1) Can divcon be launched selectively with amber (and an important option
> for
> > RESTARTING should a crash occur), or AM1 is what can be launched? It seems
> to
> > me that it is not the same thing.
>
> I believe there's some confusion here. First, note that 'antechamber'
> is the name of both a collection of programs, and a script that
> executes them in a definite order. DIVCON is one of those programs,
> which is called when the antechamber script is required to generate
> quantum information itself. This is not a required step, and others
> have already suggest to use some external program for this step, in
> place of DIVCON.
>
> DIVCON has a number of QM Hamiltonians. AM1 is one of those. So, AM1
> is *not* something "to be lauched", but rather one of the QM methods
> available in DIVCON, and in many other QM programs. DIVCON just
> happens to be the one that is plugged into the antechamber package,
> but nothing stops you of using any other, if you wish.
>
> About "Launching with Amber", we need to understand what you mean by
> that. SANDER has 2 ways of doing QM/MM: One is using DIVCON, which
> which has an interface with SANDER, and the other is using the QM
> methods provided natively within SANDER. SANDER provides, natively,
> support for MNDO, AM1, PM3, SCC-DFTB and variations of those.
>
> > (2) When launching antechamber as in tutorial B4 (the - more or less - way
> I am
> > using it), is "divide and conquer" at work? I see, during present
> antechamber
> > job, listed in divcon.out statements like "Resetting search direction".
> What
> > does that mean? That guess Hessian is recomputed from the last good
> > coordinates? Or does that mean that minimization of my molecule is done by
> > formally cutting it into pieces (divide and conquer)? The way I was used at
> > when computing charges "ab initio" via HF-6-31G* by formally cutting the
> > molecule into residues.
>
> This question is probably better answered by one of the DIVCON's
> people, but my guess is that, if it's using DIVCON, it is "divide and
> conquer". After all, that's what DIVCON means... But notice that this
> is not necessarily related to the calculation of charges. DIVCON is a
> method to solve the SCF equations by dividing the molecules into
> pieces. The nature of "divide and conquer" probably has nothing to do
> with the "resetting search direction" message. This message only means
> that whatever vector the minimizer was following is not minimizing the
> energy, and it is going to try something else. (But I'd wait for the
> DIVCON people to come in here...)
>
> > (3) Amber9 manual, after stating that divcon is called by antechamber (p
> 74),
> > refers to AM1 in the following pages, none of the many options of divcon
> > (chapter 7) being mentioned.
>
> Again, that just means they are just using DIVCON to do an AM1 calculation.
>
> > (4) When launching a QMMM procedure from sander.MPI, is the QM part running
> > parallel? If so, why not applying parallelization for the AM1 minimization
> > within antechamber?
>
> That goes back to the different implementations of QM inside SANDER
> (see above). Notice that antechamber calls DIVCON and *not* SANDER
> when it needs a minimization. SANDER is not exactly known for it's
> great minimization abilities...
>
> Also, I cannot say much about DIVCON, but the native SANDER QM
> implementation is not fully parallel yet. The greatest difficulty is
> with the parallelization of the eigenvalue solver, which is far from
> trivial. This is a problem not only in SANDER, but in most QM programs
> out there, and is a field of active research.
>
> > This is a message from a user who has to rely heavily on antechamber, and
> is
> > carrying out a job for a non-polymeric, flexible molecule made of 500 atoms
> > with a huge number of chiral centers and many charges. Just the job of
> creating
> > a pdb file was real "work". I omit discussing why I am not using an
> external
> > program parallelized in AM1. Who had ever to prepare files for MD for
> large,
> > flexible non-polymeric molecule will understand why.
>
> I just wanted to add here that, for a molecule this size, DIVCON is
> probably one of the best possibilities, since it has been built
> exactly with that in mind. I can't tell you much about parallelization
> there, though.
>
> HTH,
> Gustavo.
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Received on Sun Aug 19 2007 - 06:07:08 PDT
