AMBER Archive (2006)

Subject: [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version

From: Lee Kyung-koo (
Date: Wed Nov 01 2006 - 17:25:25 CST

Dear Walker,

Thank you for your answer.

I installed parallel version of amber9 in intel itanium server usaually called white box with intel compiler 9.
Installing amber9 went well without a error message.
When I runned QM/MM calculation with 2 process (mpich option is -np 2), it's not working.
For long time, sander don't stop itself and don't make any data.

In running with 1 cpu (mpich option is -np 1), sander are working normally.

Sincerely, yours

---------[ 받은 메일 내용 ]----------
제목 : RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
날짜 : Wed, 1 Nov 2006 13:36:17 -0800
보낸이 : "Ross Walker"
받는이 :

Dear Lee,

With regards to your first question the QM/MM code is not completely
parallelized. Although I'm not sure what you mean by just running with one
process. - where did you get the information from that it is running 1

If I explain how QM/MM currently works in parallel this might make it a bit
clearer. At present during a QM/MM simulation the whole of the MM part of
the simulation is parallel and all parts of the QM simulation are parallel
with the exception of the matrix diagonalization (see Dave I am learning ;-
)) which is done only on the master processor. For systems that have a
large MM region, a fairly small QM region (50 - 60 atoms) and use a fairly
complex QM potential (I.e. they have pme or GB turned on for QM) then you
can get some scaling to about 4 to 8 processors or so at which point the
serial nature of the diagonalization prevents any more scaling. This would
be say for 30,000 MM atoms and 50 QM atoms. If you have many more QM atoms
(>80 or so) then the matrix diagonalization dominates
so you won't see much benefit on multiple cpus.

Hence the benefits of running QM/MM in parallel really depends on the type
of simulation you are running. Typically I find on a 4 processor SMP
machine you can run reasonably in parallel for a typical QM/MM simulation
in explicit solvent.

If however, you find that it does not run in parallel at all (no atom
division data in the output file etc) then something is most likely wrong.

With regards to the peptide correction this is based on an approach that
was originally adopted in MOPAC and I believe that it is generally accepted
that you need this correction for AM1 or PM3 when dealing with peptide
linkages. Here is a discussion of it in the mopac manual:

there are also some cautions here

I am not aware if there is a paper discussing this. You may want to ask the
question on CCL to see whether MM corrections to peptide barrier heights in
semi-empirical calculations are discussed in any publications.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: [] On Behalf Of
Lee Kyung-koo
Sent: Wednesday, November 01, 2006 11:50
Subject: AMBER: Problem of QM/MM calculation with amber 9 parallel version

Dear Amber users,

I have two question about the QM/MM calculations.

First, I installed Amber 9 to a parallel version.

It's working with multi-process in simulating classical MD.

but in simulating with multi-process in QM/MM calculation, sander are not

just runing with one process.

Is it normal?

Next, I want to know about PEPTIDE_CORR option in QM/MM calculation.

I have calculated the system that consist of small QM area(peptide) and
remaining MM area.

After some time in simulation, backbone angle(omega angle) was changed to
cis form.

Usually, that peptide are not exist in cis form.

To maintain the peptide angle to trans form, I need to use PEPTIDE_CORR

I want to know why this phenomenon happen and know papers about this

Sincerely, yours

"우리 인터넷, Daum" 『평생쓰는 무료 한메일넷』

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