[gmx-users] Permeability determination

[Chetan Puri]

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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