Update, I got it solved so far, by setting back to default value maxcyc=10000, while keeping drms=0.002 (default is 0.001). A run with 200+ amino acid residues may take 12-20 hours in my case, assigning 2 frames per cpu core (mooring np -4 with 8 frames total).
Sent from my iPhone
> On Apr 4, 2020, at 2:26 PM, Liao <liaojunzhuo.aliyun.com> wrote:
>
> Thanks there, I can look into the by hand minimization method.
> The system is in total 261 residues, 2 proteins and a ligand.
> I was also planning to change drms to a larger value like 0.005 or 0.01, to see if the entropy values differ greatly than compared to 0.002 that I was using. If the values are close enough it can also be a solution.
>
> Sent from my iPhone
>
>>> On Apr 4, 2020, at 12:30 PM, David A Case <david.case.rutgers.edu> wrote:
>>>
>>> On Fri, Apr 03, 2020, Liao wrote:
>>>
>>> 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.
>>
>> This is a case where you may need to do the entropy part "by hand". I'd
>> explore using txmin.c to carry out the minimization, and tnmode.c to do
>> the subsequent normal mode analysis. (These programs are in
>> AmberTools/test/nabc; you can also use NAB versions of the same thing.)
>> Be sure you have SHAKE turned off in the minimization.
>>
>> Equally well, you can modify the sander minimization to use xmin (set
>> ntmin=3).
>>
>> Caveat: I'm not familiar with how many options you have in using the
>> MMPBSA.py scripts -- there may be option there that others on the list
>> can suggest.
>>
>> It would help to know how big your system is.
>>
>> ...thx...dac
>>
>>
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Received on Sat Apr 11 2020 - 22:00:02 PDT
