[gmx-users] Permeability determination

[Abhishek Acharya]

Hello,

What Justin means is that when you apply position restraints, you are
fixing the positions of the atoms. In this situation, whatever property you
calculate would be incorrect as
such a restrained system is simply unphysical; in real membranes atoms are
not restrained to a position. In your case, if you restrain the lipids and
pull your ligand through this membrane,
the natural (or simulated) dynamics of the membrane in response to ligand
pulling will be hindered. Thus the calculated PMF will be incorrect.

With respect to the first point, I don't know the details of your system,
but I think he means that in your case the movement of the membrane along
the z-axis does not matter since the system
is periodic; what matters is the relative movement of the ligand with
respect to the membrane.

I hope it is clear now.

Regards,
Abhishek Acharya


Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Wed, Nov 15, 2017 at 11:44 AM, Chetan Puri <chetanpuris at gmail.com> wrote:

> Without restraining the lipid the mdrun for pulling the ligand works but I
> am able to understand the concept which you have talked about in previous
> email.
>
>  " 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 "
>
> So can you please explain in more simple way .
>
> CHETAN
>
>
> On 11/14/17 9:32 AM, Chetan Puri wrote:
>
> > I am trying to do umbrella sampling for a ligand and dopc membrane.
> > For umbrella sampling pulling step, I am unable to posre_restrain the
> > lipid, since grompp gives a error due to conflict between posre_restrain
> > file of lipid and itp file of lipid.
> > I have 128dopc molecules.
> >
> > So can someone suggest how to posre_restrain the lipid.
> >
>
> http://www.gromacs.org/Documentation/Errors?highlight=
> errors#Atom_index_n_in_position_restraints_out_of_bounds
>
> I don't think you need restraints for this kind of system, as I explained
> before, but do as you see fit.
>
> -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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