[gmx-users] Determining a ligands permeability

Justin Lemkul 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 
you propose.

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.
Assistant Professor
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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