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

[Justin Lemkul]

On 8/18/19 11:28 PM, sunyeping wrote:
> Hello Bratin Kumar Das，
>
> Your answer is correst but irrelevent to my question. By adding energygrps option in the mdp and rerun the trajectory and generate the edr file containing the interation energy information which can be extracted by enemat. However enemat only gives the range of the interaction energy. My question is how to  calculate interaction energy between two groups for every frame in the trajectory.

That is precisely what Bratin is telling you to do, and his answer is 
exactly correct.

You need to use gmx energy, not gmx enemat, to get the interaction 
energy values in every frame. Then find the lowest and extract the 
corresponding frame with trjconv. Whether or not this quantity has any 
physical meaning is, however, questionable for most force fields.

-Justin

> ------------------------------------------------------------------
> From:Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> Sent At:2019 Aug. 19 (Mon.) 11:11
> To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> Subject:Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?
>
> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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