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

[Justin Lemkul]

On 1/21/20 2:01 AM, sunyeping wrote:
> 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.
>

You have to enter the groups explicitly and terminate selection with a 0.

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

Yes, because by definition 1-4 interactions are intramolecular.

-Justin

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Justin A. Lemkul, Ph.D.
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