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
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Department of Chemistry
University of Florida
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Received on Fri Apr 02 2021 - 14:00:02 PDT
