Hi Andy, thanks very much for the reply. We do have ScaLAPACK, I will give that a try. Do you have any suggestions regarding what method to use other than PM3? I've ran a couple of short simulations that show that a QM treatment results in significantly different forces during SMD runs.
________________________________
From: Dr. Andreas W. Goetz <agoetz.sdsc.edu>
Sent: Wednesday, June 08, 2016 2:16:36 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Dismal QM/MM Efficiency
Hi Colin,
This is expected behavior. The QM portion is the parallel scaling bottleneck (in particular the linear algebra, matrix diagonalization). Even with a very large MM region (which parallelizes well), it usually makes no sense to run semiempirical QM/MM jobs on more than a single node. To achieve best performance make sure that you link against well-optimized BLAS and LAPACK libraries, Intel MKL is usually good. Depending on the QM region size, you should get a performance on the order of 100ps/day. This is already pretty good.
Another question you have to ask yourself is whether a semiempirical method like PM3 will actually be good in describing the the coordination of calcium ions to carbonyl groups. This is not necessarily the case.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de<http://www.awgoetz.de>
> On Jun 8, 2016, at 11:52 AM, Nisler, Collin R. <nisler.1.buckeyemail.osu.edu> wrote:
>
> Hello, I am running a steered QM/MM simulation on a protein that binds 3 calcium atoms, and I want to model the carbonyl atoms that coordinate with the calciums using QM. I tried using the semi-empirical method built in to Amber on a parallel supercomputer with 6 nodes, 12 cores per node. I used the parallel version of sander, sander.mpi. I was getting some terrible efficiency, something much less than 1 ns/day. The system is only 3,200 atoms (I'm doing initial runs in vacuum), and the QM region consists of 62 atoms. I'm hoping there is a way to make this more feasible. Is this normal, or is there something I can do to speed up the simulation? Thanks very much.
>
>
> Input file:
>
>
> Pulling CDH23
> &cntrl
> imin = 0, cut = 10.0,
> ntb = 0, igb = 0, nscm = 0,
> ntx = 5, irest = 1, ntc = 2, ntf = 2,
> tempi = 300.,
> temp0 = 300.,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 20000, dt = 0.002,
> ntwx = 500, ntwr = 1000, ntpr = 100, ntwr = 1000,
> jar = 1, ifqnt = 1,
> /
> &qmmm
> qmmask = '.371, 372, 373, 375, 374, 376, 1631, 1632, 1633, 1634, 1635, 1636, 1613, 1612, 1611, 1614, 1589, 1590, 1591, 1592, 1593, 1594, 1155, 1156, 1157, 1158, 1159, 1160, 2128, 2129, 2130, 2131, 2132, 2133, 1653, 1654, 1651, 1652, 2102, 2103, 2104, 2105, 2106, 2107, 2856, 2857, 2858, 2859, 2860, 2861, 2179, 2180, 2177, 2178, 1620, 1621, 1116, 1117, 1118, 1119, 1120, 1121',
> qmcharge = -8
> qmshake = 1,
> qm_theory = 'PM3',
> writepdb = 1,
> /
> &wt type = 'DUMPFREQ', istep1 = 1, /
> &wt type = 'END', /
> DISANG = distqm.RST
> DUMPAVE = dist_vs_tqm
> LISTIN = POUT
> LISTOUT = POUT
>
>
>
> distqm.RST:
>
>
> # change distance between atoms 5 and 3187 from 105.10967 A to 205.10967 A
> &rst iat=5,3187, r2=105.10967, rk2=1, r2a=155.10967, /
>
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Received on Wed Jun 08 2016 - 13:00:02 PDT
