One additional thing I just realized that I didn't notice at first.
There seems to be a self-interacting component to all the forces (which I would naively guess could be called internal forces). How should these components be interpreted?
Below are the first couple of lines from the output file, where you can see the components I'm talking about. First data line has res1=1, res2=1 so the pairwise energy between residue 1 and itself (which I would say should only have an internal energy component), but instead have the opposite (no internal energy component, but non-zero components for all the other forces).
Total Energy Decomposition:
Frame #,Resid 1,Resid 2,Internal,van der Waals,Electrostatic,Polar Solvation,Non-Polar Solv.,TOTAL
1,1,1,0.0,1.03262,48.857851,-55.235707,3.4600573872,-1.8851786127999999
1,1,2,0.0,1.7566,-10.583139,2.811188,-1.3770785448,-7.392429544799
Kind Regards
Tue
------- Original Message -------
On Thursday, February 10th, 2022 at 12:44 AM, Tue <tue.boesen.protonmail.com> wrote:
> Hi
>
> I am currently comparing the energies returned when using idecomp 2 and 4, and I notice that the internal energy when computing pairwise is always 0, which I don't understand. I would expect the internal energy to be placed on the diagonal and be the same as when using idecomp 2 (so internal energy for res1=5,res2!=5 to be zero, and res1=5,res2=5 to be the same as the internal energy for res=5 with idecomp 2)
>
> So in order to get the internal energy out as well as the pairwise energy, do I have to run the script twice, with both idecomp 2 and idecomp 4? that seems weird, when I can get all other components from the pairwise by just summing up all pairs.
>
> Is this a bug or is this intended?
>
> Input file (for case 2), in case that is relevant
>
> |Input file:
> |--------------------------------------------------------------
> |Sample input file for GB and PB calculation
> |&general
> | startframe=1, endframe=9999999, interval=1,
> | verbose=1, netcdf=1,
> |/
> |&decomp
> |idecomp=2, dec_verbose=3,
> |/
> |&gb
> |saltcon=0.15
> |/--------------------------------------------------------------
> |MMPBSA.py Version=14.0
> |Complex topology file: 1ab3_0_5.prmtop
> |Initial mdcrd(s): 1ab3_0_5.pdb
> |
> |Calculations performed using 1.0 complex frames.
> |
>
> Kind regards
> Tue
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Received on Thu Feb 10 2022 - 10:00:02 PST
