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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
