Yes, I found something in the line you suggested during MD, which explains at least partially why the values jump.
Thanks a lot, very useful !!
Fabian
-------------------
Fabian Glaser
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701
> On 5 Dec 2021, at 16:04, David A Case <david.case.rutgers.edu> wrote:
>
> On Sat, Dec 04, 2021, Fabian Glaser wrote:
>>
>> I am working on agonist ranking project, computing free energy for wt and
>> mutants. I tried several MMPBSA input values, and it seems that inp=1 is
>> better than inp=2. inp=1 values give values more similar to experimental
>> values, at least for some examples.
>
> My experience is limited and quite a bit out of date, but here goes: the
> inp=2 option seems a bit more "fragile" than does the simpler inp=1 option,
> especially for absolute binding energies. I too ran into cases where inp=2
> gave very odd results, but the details are lost in the mists of time. Maybe
> Ray and folks from his group can help here.
>
>> I am running multiple trajectories, and I found the delta total values are
>> very variable with a stdev of about +-3-5, specially for the mutants. I
>> tried running very long simulations, but still the values drift a lot. I
>> also tried different sampling using 500 or 1000 frames, but it did not
>> improve the results.
>
> Answers here are surely system-specific. Try using more frames, and/or
> different length simulations. Note that you are looking for convergnence
> here, not for agreement with experiment.
>
> Be sure that your system is stable, and not always exploring new
> configurations as time progresses. Check results for (say) the first half
> of a given trajectory vs. the second half.
>
> ...good luck...dac
>
>
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Received on Tue Dec 07 2021 - 04:00:02 PST
