[gmx-users] small tc-group
chris.neale at mail.utoronto.ca
Fri Oct 12 16:52:44 CEST 2012
Use the sd integrator and specify System as the single temperature coupling group.
integrator = sd
tc_grps = System
tau_t = 1.0
ld_seed = -1
If you're doing US simulations, then you're probably not going to be looking at dynamic information in any event
so you lose nothing by doing velocity Langevin dynamics and at the same time you both eliminate the
flying ice cube problem and sample the correct ensemble (this last thing is not done when using separate
temperature coupling groups).
-- original message --
I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL
molecules per lipid, and a small highly charged peptide at certain distance
from the bilayer. I want to do a pulling simulation in order to pull the
peptide inside the membrane along the z-direction. So, taking into account
that I want to explore the differents configurations doing a serie of US
simulations, and that in some windows I have the peptide in the water bulk
and in others it is inside the hydrophobic core of the membrane (but with
some hydration water molecules), I'm wondering about what is the best
approach for define the tc-groups..?
Peptide Membrane SOL_Ions or Membrane Peptide_SOL_Ions ?
Note: when I choose the peptide separately, the temperature fluctuations are
high (between 50 and 100K approximately).
any comment would be very appreciated.
best regards, Facundo
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