[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Bratin Kumar Das]

You need to prepare one .mdp file where the energygrps = DNA Protein ( as
example). Generate the .tpr file and rerun using mdrun module.
gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc

On Mon 19 Aug, 2019, 8:09 AM sunyeping, <sunyeping at aliyun.com> wrote:

> Dear all,
>
> I am doing protein-DNA complex simulations with gromacs and I have gotten
> a trajectory. Now I want to calculate interaction energy between the
> protein and the DNA in every frame of the trajectory so that I can pick out
> a frame in which the  interaction energy between them is the largest, but I
> don't know how. I have used "enemat" , but it only gives a range of the
> energy, not every frame. The output read:
>
> Last energy frame read 5000 time 500000.000
> Will build energy half-matrix of 2 groups, 6 elements, over 5001 frames
> Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
> Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
> Matrix of total energy ranges from -21540.623047 to -2283.419434
>
> So could you tell me how to calculate interaction energy between two
> groups for every frame in a trajectory?
>
> Best regards.
> --
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