Filip,
In terms of performing dynamics, I believe the primary QM/MM module in
AMBER is and will continue to be SQM. However, this is only for NDDO and
SCC-DFTB type semi-empirical Hamiltonians.
I do not know the status of the other options, but I believe there are a
couple, including the Pupil interface (to Gaussian only?) maintained by the
Merz group and Extern that is new(er?) from the Walker group. I think
those are the only choices for *ab initio* calculations, but I could be
wrong.
Marc,
Unfortunately what you want is probably not going to be available very
soon, but in practice may not be worth the trouble anyway. The reason is
that the parallelization in SQM is currently only done or the fock matrix
build and is done by naive partitioning of the atoms across the available
processors. This means that:
1.) Once you have enough atoms (maybe like 100+?), the matrix
diagonalization routines, which are not parallelized, become the
computational bottleneck and scaling becomes unfavorable. I believe Ross
Walker investigated this rather extensively in the original paper and
showed scaling beyond 8 processors is pretty much not cost effective.
The relevant paper is: Walker, *et al.* J. Comput. Chem. 2008, 29, 1019.
2.) d-orbital atoms have 10 extra orbitals compared to p-orbital atoms
(which only have 8 total). Therefore the naive partitioning scheme is not
likely to work very well anyway because the d-orbital containing partitions
would have a considerably higher number of orbitals. This would probably
preclude good efficiency at even 2 processors, unless you were perhaps very
clever in constructing your QM residues and can trick the partitioning into
dividing the d-orbital atoms evenly (not to mention hydrogens and link
atoms, which have a similar, but smaller effect). The solution, I suppose,
would be to do the partitioning by orbitals, not atoms, but I think that
would require a considerable amount of work to change the code (even more
than what it took to implement the d-orbital, which was non-trivial).
In any event, the speed in AMBER is pretty good to exceptional compared
with the other available d-orbital QM/MM codes (I'm thinking MNDO97 and
SCC-DFTB in CHARMM, but maybe there are others). I can routinely get
100-200 ps a day with 40-100 QM atoms, 2 of which contain d-orbitals. That
may not sound like a lot, but most QM/MM umbrella sampling simulations I
see in the literature barely get more than a few 1 ps per window.
If you are wanting to run ns scale QM/MM simulations, welcome to the club!
I don't think anyone is really there yet.
Regards,
Brian
On Mon, Apr 16, 2012 at 12:26 PM, filip fratev <filipfratev.yahoo.com>wrote:
> Hi all,
> I'd like to extend the question. According to
> the Amber 12 manual it is possible to perform QM/MM using TeraChem software
> (Cuda software). However, developers of the TeraChem ensured me that this
> not
> possible at the moment and probably will be possible in June.
> Thus, which programs are available at the
> moment for QM/MM calculations?
>
> All the best,
> Filip
>
>
> ________________________________
> From: Marc van der Kamp <marcvanderkamp.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Monday, April 16, 2012 6:57 PM
> Subject: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized?
>
> Dear developers,
>
> An important reason for me to upgrade to AMBER12 was the availability of
> MNDO type Hamiltonians with d-orbitals for QM/MM (in particular AM1/d).
> Unfortunately, my first test-run with sander.MPI told me:
>
> SANDER BOMB in subroutine sander()
>
> Using d orbitals but the d orbital code is not parallelized.
>
> Please run in serial.
>
>
> The message is clear, but I'd love to run this in parallel, as QM/MM MD
> will take a looong time on a single processor.
> Is work underway to parallelize the d orbital code?
> If so, that would be great!
> And would there be an approximate ETA for this? (e.g. weeks, months or
> years from now?)
>
> Many thanks in advance,
> Marc
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Mon Apr 16 2012 - 11:00:04 PDT
