Subject: Summary of QM/MM question

From: [email-masked] (Howard Alper)
Date: Thu, 5 Dec 1996 08:51:52 -0800

Hi all,

  On Nov. 15th I wrote the ccl, asking some questions about the use of
combined Quantum/Classical forcefields (QM/MM).  My original query was:

________________________________________________________________________

  Hi all,

  I will be doing simulations using the mixed or combined quantum/classical
forcefield in CHARMM.  I have several questions, and would appreciate your
help:

1) Does anyone know of improvements in combined-forcefield codes as
regards efficiency?  I am asking because I may designate a non-insigificant
number of atoms as quantum atoms, and so the CPU time will go up drastically.

2) Does anyone know how the CPU time/md step changes as a function of the
number of atoms designated as quantum atoms?

3) Is there any information on the relative amounts of time spent on
calculating the interactions between quantum atoms, vs. the time spent
on interactions between quantum and classical atoms?

  I will summarize the results and post to the list.  Thanks.

  Howard

________________________________________________________________________

  Now here are your responses:

________________________________________________________________________

Rick Venable:

On Fri, 15 Nov 1996, Howard Alper wrote:
>   I will be doing simulations using the mixed or combined quantum/classical
> forcefield in CHARMM.  I have several questions, and would appreciate your
> help:

There's CHARMM, and then there's CHARMM; the answer is version dependent. 
There are many recent changes in this area found only in CHARMM the c25a2
version. 

> 1) Does anyone know of improvements in combined-forcefield codes as
> regards efficiency?  I am asking because I may designate a non-insigificant
> number of atoms as quantum atoms, and so the CPU time will go up drastically.

There's QM, and then there's QM; CHARMM c25a2 supports both AMPAC
(semi-empirical) and GAMESS (ab initio) codes, but only one of these may
be included in a given executable.  The determination is made at compile
time via preprocessor keywords (QUANTUM or GAMESS) in the pref.dat
configuration file.  For AMPAC (the QUANTUM keyword in pref.dat), I've
found that modifying the quantum.mk Fortran compiler options from the
default level 0 optimization to level 2 with static array storage leads to
a 4-fold speedup for the testcase; true for c24 versions as well. 

CHARMM c25a2 includes a parallel version of GAMESS, so that both the MD
and the QM portion can be run on various parallel architectures, from
workstations linked by FDDI to high end systems like the SP2 (IBM) and T3D
(Cray).  I don't believe the AMPAC code runs in parallel, though. 

> 2) Does anyone know how the CPU time/md step changes as a function of the
> number of atoms designated as quantum atoms?
> 
> 3) Is there any information on the relative amounts of time spent on
> calculating the interactions between quantum atoms, vs. the time spent
> on interactions between quantum and classical atoms?

The best person to answer these questions is Milan Hodoscek, who did a lot
of the integration of CHARMM and GAMESS, and has been instrumental in
re-designing the QM/MM interface to include such features as blurred
charges (rather than point charges) and providing a common interface for
both QM code sets.  His E-mail address is   [email-masked]

For more general info, see the c25a2 CHARMM documentation files at

http://www.mgsl.dcrt.nih.gov/Charmm/

especially the gamess.doc file.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \  /   |=|  ( Not an official statement or
[email-masked]       \/    |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/venable.html    |=|    see   http://www.fda.gov  )

________________________________________________________________________

A. J. Turner:

I am not aware of anything faster than Charmm - as Charmm is about the
only am1 implementation that I am aware of!.

At ab-initio - you can bank on all the time being in the 2 electron
integrals - so the scf/mm interaction is cheep (unless you have a very
small scf and thousands of mm atoms).

At am1 / charmm things seem quite different.  Say with 1500 mm atoms - you
need about 20 heavies and 20 lights before the scf takes longer than the
qm/mm interactions.

The plain fastest is to use non-polarised qm/mm with an scf - but that is 
not anything like as 'good'.

I hope that helps a little.

Let me know if you want anything else on the subkect

Alex

________________________________________________________________________

Milan Hodoscek:

    Howard> 3) What is your experience with the effect on the CPU time
    Howard> of using the mixed forcefield?  More specifically:

    Howard> 3a) Do you have any knowledge of how the CPU time for a
    Howard> combined-forcefield dynamics simulation goes up with the #
    Howard> atoms designated as quantum?  What other variables might
    Howard> affect this trend (connectivity between quantum atoms,
    Howard> nonbonded cutoffs, quality of quantum calculations, etc)?

The main thing is number of QM atoms. It goes like N**3

    Howard> 3b) If one can think of the quantum calculations as of two
    Howard> tpes, those between quantum atoms and those between
    Howard> quantum and classical atoms, what % of the total quantum
    Howard> forcefield calculation time is taken up with the former
    Howard> and latter calculations?  (I am assuming that the quantum
    Howard> calculation can be bnroken up into intra-quantum and
    Howard> quantum-classical.  Is this the way the calculations work?
    Howard> If not (in general) how do you they work to produce forces
    Howard> between quantum atoms and between quantum and classical
    Howard> atoms?)

Everything is coupled together and the whole calculation is performed
on each energy call, e.g. every step in the dynamics run.

Milan

________________________________________________________________________

  I thank everyone so much for their responses.

  Howard

-- 

  Dr. Howard Alper
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