[gmx-users] index file

Justin A. Lemkul jalemkul at vt.edu
Thu May 12 20:41:36 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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