Re: [AMBER] QM-MM Equilibration Step

From: Gustavo Seabra <>
Date: Thu, 18 Jun 2015 15:06:23 -0300

Hi Brittany,

On qui jun 18 2015 14:06:34 Brittany Boykin said:
> […] 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.

What kind of convergence are you referring to here? Increasing the number of steps will not change the SCF convergence, which is the problem you show below.

> 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:

The input below is already QM and, judging by the number of steps (50.000) compared to what you said above, that would be your first constant volume and pressure calculation for this system. Did you let it run for a while (equilibrate) with regular MM, at the final temperature and pressure _before_ turning on QM?

> # 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
> /
> 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

What “both”? (there’s only one input here).

> 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 often do you get this message? It only means that, for that specific MD step (47) the SCF calculation did not converge. There are a number of reasons why this could happen. Your system may be in a bad conformation, an MM solvent molecule may have entered the QM zone and be interfering with the SCF, your system may have assumed a conformation that is badly described by the method (meaning you may need to reconsider your choice of hamiltonian), etc. If this happens only occasionally during the simulation, you can probably ignore it as the dynamics will fix itself. However, if the message appears often, you must look closer into the structures to see what may be going on there. The usual advice here is the same: print out every step, and try to follow the structure of the system to see if you can identify any problem.

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Received on Thu Jun 18 2015 - 11:30:02 PDT
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