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

[sunyeping]

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.
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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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