[gmx-users] how to include multiple energy groups for interaction energy calculation?

[sunyeping]

Hi Justin,

Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the work. I still have a couple of questions: 

(1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the interaction energy, the interested energy terms should be input. Because there are four ligands in my structure, there are accordingly 16 terms, for example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24 Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37", but is there a simple syntax for this selection? I tried "22 to 37" and "22-37", but they doesn't work.

(2) I find that the values of  all  Coul-14 and LJ-14 terms are zero. Does this make any sense?

Best,

Yeping Sun
------------------------------------------------------------------
From:Justin Lemkul <jalemkul at vt.edu>
Sent At:2020 Jan. 20 (Mon.) 22:17
To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
Subject:Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?



On 1/20/20 7:58 AM, sunyeping wrote:
> Dear all,
>
> I am doing MD simulations on a protein-ligand complex. This complex has 4  protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to calculate the interaction energy between each ligand and their binding protein subunit, respectively. I include the  "energygrps" parameter in the mdp file for generating a tpr file for rerun the trajectory as following:
>      energygrps      =  Protein LIG1
>
> This seems to work fine. However, could it be possible to include all four ligands in the "energygrps" parameter and rerun the trajectory once to get the interaction energy between all the four ligands and their respective binding protein subunit? I tried to write the "energygrps" parameter as following:
>    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein LIG4
> and run the "grompp" command:
>       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
> I received the following error:
>      Fatal error:
> Group LIG1, referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> I am sure that LIG1 is included in the index file. This error is most probably caused by the incorrect input of the "energygrps" parameter in the mdp file.
>
> So I wonder whether it is possible to include multiple energy groups in the mdp file or I have to rerun the trajectory four times to get the interaction energy for the four ligands?

The list of energygrps should not be comma-delimited. You should specify:

energygrps = Protein LIG1 LIG2 LIG3 LIG4

and this will generate a full matrix of interactions among all four 
species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you 
but this is how you get all of the interaction energies with the protein 
in one shot.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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