[gmx-users] Position restraining protein during equilibration stage

[Agnivo Gosai]

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 ?

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


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.