Perfect, thank you!
> On Aug 15, 2016, at 5:11 PM, David A Case <david.case.rutgers.edu> wrote:
>
>> 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 Tue Aug 16 2016 - 07:00:02 PDT
