[gmx-users] Position restraining protein during equilibration stage
agnivogromacs14 at gmail.com
Tue Nov 4 23:37:22 CET 2014
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
Grad Student, Iowa State University.
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