[gmx-users] Determining a ligands permeability
jalemkul at vt.edu
Mon Nov 6 12:54:48 CET 2017
On 11/6/17 12:22 AM, Du, Yu wrote:
> Hi, Justin,
> Thanks for your question. Presume that ligands were in only one side of the box outside of the membrane.
> 1)In metadynamics, the membrane will be pushed by the ligands. After long time simulation, the membrane may move along the Z-axis.
> 2)In steer MD, one ligand will be pulled across the membrane and the membrane can also moves along the Z-axis.
> This is the reason that I said some POSRES should be applied on the Z-axis of the lipids.
> So, what is your opinion, Justin?
I disagree. Who cares if the lipids move? The reaction coordinate is the
relative distance between the ligand and membrane COM. In a periodic
system, the "center" is arbitrary as is the "sidedness" of the system
If you restrain the lipids, you perturb their dynamics and likely
influence the free energy of permeation across the membrane. It's not
wise. A sufficiently slow/gentle pull across the membrane should not
significantly perturb the membrane in any detrimental way. I've seen
this done many times.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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