Hi Adrian,
I am using below[1] script for 1-7 part.
And yes I just realized I counted the "frame 3" twice in all of the cases considered. Can that produce so much difference in results?
[1]
Per-residue GB and PB decomposition
&general
endframe=7, verbose=1,
/
&gb
igb=5, saltcon=0.00,
/
&pb
istrng=0.00,
/
&decomp
idecomp=1,
dec_verbose=1,
/
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
> On Apr 2, 2021, at 4:30 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
> Just to make sure
>
> if you split 1-3 and 3-10, you are counting frame 3 twice.
>
> Can you clarify what you did ?
>
> Also, are you doing entropy calculations also? If so, those are not
> additive by frames unless you are VERY careful on how you do it.
>
>
> adrian
>
>
>
> On 4/2/21 4:23 PM, Jatin Kashyap wrote:
>> [External Email]
>>
>> Hi David,
>>
>> I did following test study: I had produced a shorter version of 6000 frames .nc file by using trajout cpptraj subroutine to produce 10 frames .nc file which I used in the following test cases.
>>
>> Study 1 >> Frame 1-10 > GB = -47.601 , PB = -6.2504
>> Study 2 >> Frame 1-3 > GB = -47.0283, PB = -5.4966 , Frame 3-10 > GB = -47.2521, PB = -6.1103
>> Study 3 >> Frame 1-5 > GB = -46.6376, PB = -5.0888 , Frame 5-10 > GB = -48.1015, PB = -6.686
>>
>> In Study 2 & 3 I used the same 1-10.nc of Study 1 to split it into 1-3&3-10 and 1-5&5-10 frames .nc respectively.
>>
>> They doesn’t add up to same value.
>>
>> ——
>> Jatin Kashyap
>> Ph.D. Student
>> Dr. Dibakar Datta Group
>> Department of Mechanical and Industrial Engineering
>> New Jersey Institute of Technology (NJIT)
>> University Heights
>> Newark, NJ 07102-1982
>> Phone- (201)889-5783
>> Email- jk435.njit.edu
>>
>>> On Mar 31, 2021, at 8:23 AM, David A Case <david.case.rutgers.edu> wrote:
>>>
>>> On Wed, Mar 31, 2021, Jatin Kashyap wrote:
>>>> I never did the solution number 3.
>>>>> I would stick with one core, and use parallelization to farm the snapshots
>>>>> out to a number of separate jobs, all running at the same time.
>>> MM-PB/GBSA is completely linear. If you analyze half of your snapshots in
>>> one job, and the other half in a second job, you can just add up the
>>> results. Same for a division of the frames into a smaller number of
>>> subframes.
>>>
>>> ....dac
>>>
>>>
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>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Fri Apr 02 2021 - 14:00:03 PDT
