Re: Constant Force Pull

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Dec 13 2018 - 07:06:12 CST

My advice would be to just pull on the ligand with a counter-force on some
protein atoms, distributed around the binding site. There should be no need
for any restraint on the membrane, that's a symptom that something else is
very wrong.

Jerome

On Thu, 13 Dec 2018 at 10:48, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I am trying to do a constant force pull on my ligand, pulling it out of
> a protein. I have the backbone atoms and certain atoms in the DMPC
> membrane constrained. The force on the ligand is 1 kcal/mol/A^2 or 69.479
> pN A. As the ligand is moving, the waters on both sides of the membrane
> expand away from the membrane the simulation stops with the error:
>
>
> ERROR: Constraint failure in RATTLE algorithm for atom 60956!
> ERROR: Constraint failure; simulation has become unstable.
>
> Before I put a constraint on the membrane, it was separating in opposite
> directions along the z-coordinate. As for the water, I can't constrain
> those or the simulation stops with periodic boundary errors. How do I do a
> constant force pull on a ligand in a protein/membrane/water system?
>
>
> *Kelly L. McGuire*
>
> *PhD Candidate*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

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