[gmx-users] Determining a ligands permeability

[Chetan Puri]

Thanks for the reply,
But I could not understand what you want to say,
Since I am trying to do the ligand and membrane simulation while
constraining
the lipid

CHETAN
On 6 Nov 2017 5:24 pm, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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