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, /
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 08 2016 - 12:00:02 PDT
