I am conducting QM-MM using AMBER for my methyltransferase systems. I am having some trouble on the equilibration of the system for constant pressure and temperature. I used NSTEP: 50,000, dt= 0.001 with time step of 1fs first after running calculation for constant volume. I then increased the steps to 500,000 to see is the calculation would converge. I took the complex structure from the MM simulation as the initial structure, QM/MM was run. I first ran the MM energy minimization, then carried out the heating progress:
# Write input below
cat > mdin << EOF
Constant pressure constant temperature equilibration stage 2
&cntrl
imin=0, nstlim=50000, dt=0.001, ntx=5, irest=1, ntpr=1000, ntwr=10000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0, ig=-1,
ntb=2, ntp=1, taup=2.0,
ntc=2, ntf=2,
cut=10.0, iwrap=1, ifqnt=1
/
&qmmm
iqmatoms=1883,1884,1885,1886,1887,1888,1889,1890,1891,2038,2039,2040,2041,2042,2043,2044,2045,2046,4317,4318,4319,4320,4321,5319,5322,5323,5324,5325,5326,5327,5328,5329,5330,5331,5334,5343,5344,5345,5383,5386,5387,5388,5389,5390,5391,5392,5394,5395,5396,5397,5398,5399,5400,
qmcharge=0,
qm_theory='PM3-PDDG',
qmshake=1,
qm_ewald=1, qm_pme=1,
diag_routine=0,
writepdb=1
/
EOF
In both cases the system did not fully converge, as I keep receiving this Warning, shown below, several times. Also, the calculation completely ran in both cases
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = -0.8514E+06 DeltaE = 0.1002E+02 DeltaP = 0.1050E+00
QMMM: Smallest DeltaE = 0.2486E+01 DeltaP = 0.6844E-01 Step = 47
How can I fix this problem for each system so that I can continue to umbrella sampling?
Thank you in advance?
Brittany Boykin
Graduate Student
Auburn University
Department of Chemistry and Biochemistry
e: bzb0031.tigermail.auburn.edu
c: (404)545.1036
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Received on Thu Jun 18 2015 - 10:30:03 PDT
