--- Seth Hayik <hayik.ufl.edu> wrote:
>
> 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, 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.
Now that sander.MPI is launched correctly "mpirun -nc 4
$AMERHOME/exe/sander.MPI ...." for a QM-MM procedure (AMBER9) with AM1 for a
98-atoms non polymeric molecule in "TIP3PBOX 15", with parameters and topology
fro Antechamber, please see below what "top -i" steadily says about the first
listed node:
USER (fr), PR(25), NI(0), VIRT(251m), RES(28m), SHR(from 10m to 7000), S(R),
%CPU(100), %MEM(0.2), TIME(...), COMMND(sander.MPI)
about the same for the other three nodes. The small %MEM for node reflects the
availability of 4GB per node. As Ross warned, it might be that reducing
drastically the available memory per node (being mainly used for "ab initio"
calculation, things are set so that all available memory can be used) might
accelerate the procedure. One has to know how the program works to judge about
that.
Increase in speed with respect to previous quite similar runs, where I had
forgotten to state "mpirun -nc 4", is about 10-20%. From DivCon manual one
learns that parallelized and non parallelized versions are released. Which one
here I was unable to find out.
You can better reach your conclusions that if I make any comment. In fact, this
report is simply in the hope that it helps other users of QM-MM.
francesco pietra
>
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Received on Sun Aug 19 2007 - 06:07:35 PDT
