[gmx-users] Determining a ligands permeability

Du, Yu duyu at sioc.ac.cn
Mon Nov 6 13:22:55 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

Thanks, Justin. I accept your convincing viewpoint that there shouldn't be any POSRES in the system.

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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