[gmx-users] Determining a ligands permeability

[Justin Lemkul]

On 11/5/17 7:40 AM, Du, Yu wrote:
> Hi,
>
> I don't study the membrane permeability of small molecules and can't give related papers.
>
> All in all, you need to first successfully simulate the lipid-small molecule system and then enhanced sampling because of the time scale of ligand diffusing across the membrane.
>
> There are some approaches to study it, such as, Metadynamics and steer MD.
>
> For Metadynamics, you can use the PLUMED with GMX and exercise larger confining potential if the ligand further away from the membrane in the water. Then, compare the chance or time that one ligand can penetrate across the entire or in the half of membrane. You can add excessive ligands in the water.
>
> For steer MD, you can follow Justin's tutorial. In both approaches, lipids should be under some position restraints.

Why would the lipids need to be restrained in this case? I would argue 
the opposite. It's a spurious force in this case.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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