jalemkul at vt.edu
Thu May 31 19:23:38 CEST 2018
On 5/31/18 1:18 PM, Amin Rouy wrote:
> Hi everyone,
> The results of simulation show all quantities are at equilibrium, like
> energies, temperature, density, etc. But RMSD is increasing all the time
> and not reaching an equilibrium.
> Does it mean should I wait longer?
Thermodynamic properties converge quickly. Dynamic properties do not
necessarily. Temperature converges within a few ps, but a protein's
dynamics may take thousands or millions of times longer to converge.
Don't rely solely on RMSD to make this assessment; it is a degenerate
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users