Thanks there, so does that mean I can raise the set drms value to larger one, without problem? Because I remember the default is 0.001, and I’ve raised it to 0.002 already.
> On Apr 3, 2020, at 6:55 PM, Roitberg,Adrian E <roitberg.ufl.edu> wrote:
>
> That has nothing to do with the normal mode calculation per se. The problem is the optimizer. For a large system, it is very hard to locally optimize the structures enough to be able to trust the low frequency vibrations.
>
> Sent from my iPad
>
>> On Apr 3, 2020, at 19:43, Liao <liaojunzhuo.aliyun.com> wrote:
>>
>> [External Email]
>>
>> Dear Amber users,
>>
>> I’ve been running into a persistent problem that I have never really resolved. That when using the MMPBSA.py.MPI script for energy calculations, specifically the nmode entropy calculations part, it very easily gets stuck.
>>
>> With drms=0.002, maxcyc=1000, I can see that in the nm.out file that gets stuck (usually stuck already by 200ns), the RMSG will go back and forth between a certain value, and never reach the drms value set. Whether maxcyc=1000 or 10000 doesn’t help, it usually gets stuck by iteration 200 or so.
>>
>> If all frames are good, they finish in an hour or so. When a single frame has this problem, after a few hours, it finishes with an error, but it still saves a result file, minus one (stuck) entropy frame. But there are times when more than one frame is stuck and nothing gets saved after a few hours.
>>
>> Have others been also getting this problem, frequently? If so, is it the structure problem, or a calculation set up problem?
>>
>> Many thanks.
>>
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Received on Fri Apr 03 2020 - 19:00:03 PDT
