normal membrane protein helix bent in Elnedyn simulation

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9 years 9 months ago #4147 by djpittdj
Dear MARTINI users:
I'm running simulations on a membrane protein which has multiple helices, but I noticed that during the simulation, the transmembrane helix can be bent compared to its original structure. Is this something expected from MARTINI? If I want to maintain the helical structure with respect to its original form, what can I do? For example, using RMSD restraints?
In the figures you can see the bent helix:
s663.photobucket.com/user/djpittdj/media....png.html?sort=3&o=0
The figure compares the original structure of the helix (yellow) and the helix after about 160.0 ns of simulation (green).
Specifics of my setup:
I used martinize.py version 2.4 to convert all-atom model to CG model.
Force field elnedyn22, rubberband force field (i.e., -ef in martinize.py): 1000
Before production run I energy minimized the system and equilibrated it with position constraints on backbone beads. Production run parameters:
dt = 0.01
nsteps = 500000000
nstxout = 0
nstvout = 0
nstlog = 5000
nstxtcout = 10000
xtc-precision = 100
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = Protein POPC W_Ion
tau-t = 1.0 1.0 1.0
ref-t = 310 310 310
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau-p = 12.0 12.0
compressibility = 3e-4 3e-4
ref-p = 1.0 1.0
comm-mode = Linear
comm-grps = Protein_POPC W_Ion
gen-seed = -1
gen-temp = 310
ld-seed = -1
Thank you very much.
Jian

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9 years 9 months ago #4148 by Clement

I'm running simulations on a membrane protein which has multiple helices, but I noticed that during the simulation, the transmembrane helix can be bent compared to its original structure. Is this something expected from MARTINI? If I want to maintain the helical structure with respect to its original form, what can I do? For example, using RMSD restraints?


Helices can bend indeed... It's not a Martini thing, it's a general dynamical behavior. As a matter of fact, Martini helices are quite stiff (long elastic bonds) and should thus bend less.

If you want to constrain your conformation. a first step is to use ElNeDyn as you did (quite heavy on the structure, meaning if it bends it's because it REALLY wants/needs to).

In the figures you can see the bent helix:
s663.photobucket.com/user/djpittdj/media....png.html?sort=3&o=0
The figure compares the original structure of the helix (yellow) and the helix after about 160.0 ns of simulation (green).


Indeed it's a behavior I would expect from such a conformation. Nothing weird here. Are you comapring with atomistic simulations? I'm pretty sure the extend of this movement would be drastically larger.

Specifics of my setup:
I used martinize.py version 2.4 to convert all-atom model to CG model.
Force field elnedyn22, rubberband force field (i.e., -ef in martinize.py): 1000
Before production run I energy minimized the system and equilibrated it with position constraints on backbone beads.


All good! And the force on your elastic network is default.

Production run parameters


Don't see any peculiar things in there. Depending on the extent of your protein outside of the membrane you could (temperature) couple it with the membrane itself, or not.

Anyway, in a few words, I would guess that's what you should expect from your system, Martini or atomistic simulations...

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