Hi Adrian, thanks for the reply. You actually brought up another question I had. The atoms that I was thinking would be negative are the oxygens in aspartate or glutamate residues. I wasn't sure if this is correct, because even though they would have a negative charge physiologically, it still wouldn't be a full negative charge since they are all paired electrons. Would they all be 0 charge then? Thanks.
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Wednesday, June 08, 2016 2:14:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Dismal QM/MM Efficiency
Hi
First, are you sure your total QM charge is -8? Seems awfully large for
62 atoms. Even if correct, QM in highly charged states (specially
anions) should be handled with extreme care.
Second, please note that you are doing 1 ns/(0.002 ps/step) = 500,000
thousand QM calculations per day in 62 atoms. Agree, we would all love
to have more, but that is a LOT of calculations.
Third, did you check scaling? It is not obvious to me that 62 atoms in
6x12 cores scales in any meaningful way. In fact, I am pretty sure it
does not.
adrian
On 6/8/16 2:52 PM, Nisler, Collin R. 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Jun 08 2016 - 12:30:04 PDT
