On Mon, Aug 15, 2016, Corum, Katharine W wrote:
>
>
> I am trying to run a QM/MM calculation on some proteins using Amber16. I
> did the NMA tutorial and I based my calculation off of that. After I
> ran the first protein (output on the left in the image at the bottom)
> I thought the QM region of the structure was optimized due to the fact
> that the output says final results. I was excited and moved onto more
> calculations (middle and right image). However each calculation stops
> at NSTEP 2114. I don't think this is a coincidence. I think I need to
> restart the calculation from the rst file but I am not sure how to do
> that. Is that what I should do since I don't think the QM region is
> optimized? Below is the input file. I used the same parameters for all
> 3 calculations but the qmmask value differs for all 3. I also put each
> protein into a box of water molecules using tleap.
Your minimization job requests 2000 steps of steepest descent, followed
by conjugate gradient minimization: the latter is more effective, but can
readily fail when SHAKE is turned on. I'm guessing that it happens to fail
after 14 steps (total steps of 2014) in each case.
You can restart a QM/MM calculation in the same way as any MM-only simulation.
But it is unlikley to change much. I'd suggest do a restart, and turning
off SHAKE: probably starting with the qmshake parameter, but also playing
with the ntc/ntf pair. (The former controls the QM region, the latter the MM
region.) Your system may already be optimized well enough to continue to MD.
...good luck...dac
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Received on Mon Aug 15 2016 - 09:30:04 PDT
