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

From: Biplab Ghosh <ghosh.biplab.gmail.com>
Date: Mon, 11 Jan 2021 10:57:36 +0530

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

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:

    imin=0, irest=1, ntx=5,
    ntt=3, gamma_ln=1.0, temp0=310.0,
    nstlim=50000000, dt=0.002,
    ntc=2, ntf=2,
    barostat=2, ntp=3, pres0=1.0,
    csurften=3, gamma_ten=0.0, ninterface=2,

Thanking you
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Received on Sun Jan 10 2021 - 21:30:02 PST
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