Hi Adrian,
I had used the mmpbsa_per_res_decomp.in script following the tutorial[1] and, it is not doing the entropy calculations.
Thank you.
[1]
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
——
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 4:43 PM, Jatin Kashyap <jk435.njit.edu> wrote:
>
> 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 <mailto:jk435.njit.edu>
>
>> On Apr 2, 2021, at 4:30 PM, Adrian Roitberg <roitberg.ufl.edu <mailto: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 <mailto:jk435.njit.edu>
>>>
>>>> On Mar 31, 2021, at 8:23 AM, David A Case <david.case.rutgers.edu <mailto: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 <mailto:roitberg.ufl.edu>
>> 352-392-6972
>>
>>
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Received on Mon Apr 05 2021 - 16:00:02 PDT
