Dear David,
thank you so much for your hints.
I am trying to perform the stability calculation you suggested
with MMPBSA.py.
I am using the GB method that, as far as I have read in the tutorial,
should be
much faster than PB.
However, despite my system is pretty small (~1500 atoms), the snapshot I am
considering is
just one and the energy contribution I want comes only from ~800 atoms, my
calculation is taking
quite long time (hours on 28 Intel Xeon processors).
Below you find the input of MMPBSA.py and the submission command I used. Am
I doing some mistake?
Thank you again for you help,
Kind Regards
Daniele
----------------------------------------------------------------------------------
*Sample input file with decomposition analysis*
*&general*
*startframe=1, endframe=2, interval=1,*
*/*
*&gb*
*igb=5, saltcon=0.0*
*/*
*&decomp*
*idecomp=4, dec_verbose=1,*
*print_res=680-690*
*/*
*----------------------------------------------------------------------------------*
*mpirun -np 28 MMPBSA.py.MPI -i mmgbsa.in <
http://mmgbsa.in> -o
FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -cp solvated.prmtop -y
prod.mdcrd*
*----------------------------------------------------------------------------------*
2018-05-22 14:12 GMT+02:00 David A Case <david.case.rutgers.edu>:
> On Mon, May 21, 2018, daniele selli wrote:
> >
> > I am pretty new in the AMBER community and I am now facing an issue with
> > the decomposition of the total energy.
>
> Just a caution: Amber force field energies are not "pairwise
> decomposable", and cannot be divided into to pieces representing parts
> of the system. There are some ways to make approximations that get
> around this, but even then, one has to make some rather arbitrary
> assumptions (e.g. assigning the interaction terms between A and B to go
> half to A and half to B.)
>
> > PS: googling I have just found people calculating binding free energy
> > with mmpbsa.py, but this is something different from what I want.
>
> Assuming I haven't talked you out of doing this :=), tell MMPBSA.py that
> you want to do a "stability" calculation: see section 31.3.4 in the 2018
> Reference Manual.
>
> ...regards...dac
>
>
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Received on Wed May 23 2018 - 05:30:03 PDT
