Steven Neumann wrote:
Dear Gmx Users,
My system includes: ions, water, two tubes made of carbon atoms, protein.
I would like to run NVT (and then NPT) with position restarined dynamics
of my protein and tubes.
I am wondering whether this approach is good (two coupling groups:
Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on
tcoupl = V-rescale ;
tc_grps = Protein_Tubes Water_and_ions ; two coupling groups
tau_t = 0.1 0.1 ; time constant
ref_t = 298 298 ; reference temperature
Please, let me know whether this apporach is ok. How can I set tc_grps
when I want to add ligand?
I don't know a definitive answer here, so I'll throw out some ideas and
hopefully stimulate some discussion. I create tc_grps based on species whose
dynamics are intimately linked. For solvent, that includes water and ions. Are
your protein and tube physically associated? If not, it doesn't make sense to
me to couple them together. In reality, no group should ever be coupled
independently, but limitations in thermostats make it necessary.
Regarding the ligand, where is it? Floating around in solvent, bound to the
protein, or in the tube? The answer to that question motivates how you treat it.
-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
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