[gmx-users] Position restraining protein during equilibration stage

Justin Lemkul jalemkul at vt.edu
Wed Nov 5 13:29:05 CET 2014

On 11/4/14 9:15 PM, Agnivo Gosai wrote:
> 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
> matter.

For movies you can do whatever you like.  For actual analysis, one normally 
discards significantly more than a few ps, or even 1 ns, but the actual amount 
of time is totally dependent upon what the system is and how long the initial 
unrestrained relaxation takes.  You have to do analysis to assess convergence of 
dynamic properties to be able to say how long this time period is.


> 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


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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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