[gmx-users] index file

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear users,
> 
> Firstly thanks for your replies. I have two ligands as I said before.
> I will analyze the system together ligands after the simulation is finished.
> For example:
> I want to plot potential energy of all system (that is, 
> protein+LİGA+LİGB) by g_energy.

This is not your whole system.  Per the snippets below, you have water and ions, 
as well.  You cannot decompose the potential in this way.

> Then,
> Should I create the groups as the following?
> 
> *energygrps      = Protein    LİGA_LİGB*
> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
> 

This will break down short-range nonbonded interactions (and nothing else!) 
between protein, LIGA_LIGB, and the rest of the system.

> OR
> 
> *energygrps      = Protein    LİGA    LİGB*
> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
> 

This will give you a decomposition between protein, LIGA, LIGB, and the rest of 
the system.  Choose whichever is most appropriate for you.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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