Peter C. Lai wrote:
I was looking at the g_membed paper recently, and noticed the authors "only"
spent 10ns to re-equilibrate the membedded-system after g_membeding.
This they also did after bumping the temperature from 300 to 323K "to prevent
ordering of the bilayer" even though the "typical" simulation temperatures of
POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it
to the DOPC environment or something?
I can't comment on this, but it seems odd to me, too.
I noticed for my particular system, I had to run a round of EM on the
post-membedded system in order to resolve some clashes before I could mdrun.
Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on
the helix CA atoms. I am inferring that because the membrane patch I used had
been previously equilibrated after I constructed it and ran it under NPT at
300K for 100ns, 10ns should be sufficient time to re-equilibrate with the
protein in the middle and 310K temperature?
I generally find that membrane protein systems need at least 20 ns or so to
really be equilibrated, but perhaps your system is a bit different. 10 ns is
about the shortest time you can use to start seeing translational relaxation
(rotational relaxation of lipids is shorter, roughly 5 ns).
After the 10ns with protein restrained, I ran Grid_MAT on it and got a
reasonable APL (61-62A^2/lipid when taking protein atoms into account,
comparable to pre-g_membed patch) and the box dimensions look stable. Is
this sufficient to answer the abvove question?
Could be. Seems reasonable.
Now I am going to be introducing a ligand to the protein. Is there a way to
preserve any state, like velocities of all the previous atoms? I was thinking
of the doing the EM while freezing everything but the ligand atoms and
allowing the ligand to change conformation (like a docking refinement). After
this, can I have the thermostat and barostat rescale the original velocities
(and gradually heat the ligand) instead of reinitialising everything?
I doubt it. By introducing new atoms into the system, you can't use a
checkpoint file any more so you lose the state you had before. You can preserve
velocities in a .gro file, but I can't think of a reasonable way to have those
read (while not having velocities for the ligand) and then heat up the ligand.
You'd have to use "gen_vel = no" in conjunction with simulated annealing, which
sounds like a recipe for instability. Is there any particular reason you think
a specific set of velocities is required? Random sampling is all part of
running proper simulations, so you need multiple, independent states to converge
to get a reliable result, anyway.
-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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