[AMBER] QM-MM Equilibration Step

From: Brittany Boykin <bzb0031.tigermail.auburn.edu>
Date: Thu, 18 Jun 2015 17:06:34 +0000

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
  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
  qm_ewald=1, qm_pme=1,

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: 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
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