Hi Seth:
Thanks. read below, please.
--- Seth Hayik <hayik.ufl.edu> wrote:
> I'm not an expert on antechamber either, but I'll try to shed
> whatever additional light I can.
>
> Firstly, most everything that Gustavo said is correct, AM1 is just
> a Hamiltonian that Divcon uses. From what I gather what you're
> trying to do with antechamber is completely separate from the
> QM/MM implementations you're trying, so SANDER won't get used at
> all.
>
> (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.
>
> Divcon is, at its heart, a stand-alone application. The version
> included in SANDER has been stripped down to use only certain
> keywords and methods that are needed in antechamber, so I don't
> think that the included divcon would work properly.
>
> (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.
>
> As Gustavo said, "resetting search direction" has to do with the
> minimizer, nothing with the divide and conquer approach. While
> Divcon is capable of divide and conquer calculations I don't think
> that these are default within antechamber.
> Divcon can do
> standard, ie. non divide and conquer which is default, or divide
> and conquer through keywords in the input file.
That "resetting search direction" was meant to searching a better path was also
my preferred view. Also,as to "divide and conquer", in divcon.out I don't see
any explicit specification about divide and conquer. However, setting the
temperature (as it occurs when launching antechamber as in tutorial B6,
TEMPK=1000.0) is a feature of divide and conquer (Amber9 manual, p. 219).
Clearly, we need that be clarified by developers who know antechamber and
divcon.
In my view, the worst about present implementation of divcon in antechamber
(Amber9) is lack of keywords DUMP=int PDUMP=int SNAPGEOM as from divcon.out,
unless they can be set (how?). This is the main need by users of antechamber
for heavy work. Launching antechamber as in tutorial B6 is risky: if it
crashes, all work is lost.
> As I said, I'm
> not an antechamber expert so I'm not sure if there is a way to
> turn on this functionality in antechamber. Also, the divide and
> conquer algorithm doesn't exactly cut the molecule into pieces,
> you can see more on how it works in: Dixon, S.L. and K.M. Merz, F
> Journal of Chemical Physics, 1997. 107(3): p. 879-893. if you're
> interested.
>
> 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.
>
> As Gustavo said, this refers to using Divcon to do a calculation
> with the AM1 Hamiltonian.
>
> (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?
>
> When you are using QM/MM you are probably using the native QM code
> for your simulations and this is not related to using antechamber.
> Divcon has some parallelization, but I don't know how it applies
> in antechamber,
Probably it could be, as the directives MPI_IS_ON and MPI_NOMC were not defined
(as from divcon.out) in present compilation of divcon for antechamber.
and you shouldn't need it for a molecule this size
> if the divide and conquer algorithm works within antechamber. I
> don't know how/if that can happen, maybe someone that knows more
> about antechamber can help you there. Another option might be to
> loosen the minimization criteria by setting XTEST, ETEST and/or
> GTEST to higher values at the expense of a less accurate minimized
> structure. This can be done using the -mk keyword(p. 75 in the
> manual), but you must specify the entire input file then, so you
> might want to look at the other keywords already in the divcon.in
> file.
>
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Received on Sun Aug 19 2007 - 06:07:09 PDT
