[gmx-users] Position restraining protein during equilibration stage

Agnivo Gosai agnivogromacs14 at gmail.com
Wed Nov 5 03:16:02 CET 2014

On the answer to Q (B) as in trailing mail :

Is this the reason we may discard say 1st few ps or even 1 ns of my
unrestrained production run outputs while plotting results or making the
movies ? During the initial time steps may we say that the unrestrained
biomolecule is kind of equilibrating during the production run ?

Kindly explain.

My reasoning so far is inferential , but I am searching literature on this

On 11/4/14 5:37 PM, Agnivo Gosai wrote:

> Dear Users
> I have followed several GROMACS tutorials , specially the excellent Lemkul
> tutorials. I have seen that during NVT / NPT equilibration states the
> biomolecules like protein / nucleic acids are position restrained.
> The general reasoning is that random velocities during equilibration can
> distort the structure of the biomolecules.
> During production run the restraints are released. But , I came across a
> case where initially a restrained NVT equilibration is done followed by a
> short un-restrained NVT equilibration. Then they directly proceed to a
> production run with a NPT-styled mdp file.
> So , my questions are ;-
> (A) When we are doing equilibration with restrained biomolecules are we not
> equilibrating the biomolecule and instead only equilibrating the solvent ?
Well, a restraint is only a biasing potential, so the restrained molecule
can move, but the amount that it moves is limited.  The solvent reorganizes
a lot during equilibration, but there are interactions between the solvent
and restrained molecule that optimize during this time.

 (B) When we remove position-restraining for the production runs are there
> no energy artificats that arise ?

There is a reason that data analysis doesn't begin at t=0.  A period of
time is still required to allow fully unrestrained equilibration.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Thanks & Regards

Agnivo Gosai
Grad Student, Iowa State University.

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