Re: [AMBER] Lateral movement of membrane bound protein during MD simulation in Amber

From: Stephan Schott <>
Date: Mon, 11 Jan 2021 12:21:37 +0100

Well, unless you have any reason to believe this motion is unnatural
enough, there is nothing intrinsecally wrong with the protein moving to the
border of the system. You have to consider that you are probably using PBC,
so it is totally fine if the protein reaches the boundary of the box; you
might want to consider removing the iwrap flag though, as more often then
not it causes more troubles then anything later on. That said, it is also
to be expected that you have somewhat more changes during the first 50-100
ns of a membrane simulation, as the system as a whole has to relax. If you
want to just remove the motion to analyze the trajectory, you can image
your system so that the protein "stays in the center" (it will just show
the relative motions of the system with respect to the protein). If for any
reason you think the motions of the protein are just too high and you would
like to hinder that, you could experiment with positional restraints for
example (check the restraint_wt flag in the manual), but again, the
diffusion of membrane components along the membrane plane are to be
expected (within ranges according to the size of the component).
Best regards,

El lun, 11 ene 2021 a las 6:30, Biplab Ghosh (<>)

> Dear Amber users/developers,
> My problem consists of a lipid bi-layer (DMPC) into which a protein (with
> transmembrane and intracellular components) is embedded. The system was
> prepared using the CHARMM GUI. I am using Amber18 for MD simulation of this
> system.
> After 100ns of MD, what I found is that the membrane-bound protein is moved
> laterally on the DMPC bi-layer. To begin with, the protein was placed at
> the center of the bi-layer with the principal axis of the protein along the
> Z-axis which is also perpendicular to the surface of the membrane. After
> 100ns, the protein has moved almost to the edges of the membrane.
> I do not want the protein to move around across the membrane. Could anyone
> please point out what is wrong with the input and how to circumvent it? The
> input for the production run in Amber is as under:
> &cntrl
> imin=0, irest=1, ntx=5,
> ntt=3, gamma_ln=1.0, temp0=310.0,
> cut=10.0,
> nstlim=50000000, dt=0.002,
> ntc=2, ntf=2,
> iwrap=1,
> barostat=2, ntp=3, pres0=1.0,
> csurften=3, gamma_ten=0.0, ninterface=2,
> /
> Thanking you
> Biplab
> --
> _______________________________________________
> AMBER mailing list

Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Mon Jan 11 2021 - 03:30:03 PST
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