Re: [AMBER] Total Energy Decomposition

From: daniele selli <>
Date: Wed, 23 May 2018 14:06:43 +0200

Dear David,

thank you so much for your hints.
I am trying to perform the stability calculation you suggested
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 and the submission command I used. Am
I doing some mistake?

Thank you again for you help,
Kind Regards

*Sample input file with decomposition analysis*
*startframe=1, endframe=2, interval=1,*
*igb=5, saltcon=0.0*
*idecomp=4, dec_verbose=1,*

*mpirun -np 28 -i <> -o
FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -cp solvated.prmtop -y


2018-05-22 14:12 GMT+02:00 David A Case <>:

> 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, but this is something different from what I want.
> Assuming I haven't talked you out of doing this :=), tell 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
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