Hi Adrian,
I had performed the calculation again by splitting the 1-10 trajectory into
1-3 and 4-10. And results changed by +/-1% from older values but they are
not adding up lenearly.
I am not performing entropy calculations, and followed the official Amber
tutorial[1].
[1]
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
On Fri, Apr 2, 2021 at 4:31 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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--
Regards,
Jatin Kashyap
DDLab
Mechanical and Industrial Engineering Dept.
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
(Phone) 201-889-5783 <(201)%20889-5783> (MEC 333H)
(Email) jk435.njit.edu
(Webpage) https://web.njit.edu/~jk435/
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Received on Wed Apr 07 2021 - 19:30:02 PDT
