[gmx-users] Determining a ligands permeability

[Justin Lemkul]

On 11/9/17 11:44 AM, Chetan Puri wrote:
> 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

Constraints and restraints are different. My advice is to not apply any 
form of *position restraints* to the lipids. You can, of course, 
constrain bonds in the lipids.

-Justin

>
> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
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-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================