[gmx-users] Position restraints do not work with steepest descent

Justin Lemkul jalemkul at vt.edu
Thu Mar 15 18:00:58 CET 2018

On 3/15/18 11:55 AM, Dawid das wrote:
> Dear Gromacs Users,
> I have used 1000 kJ/(mol*nm^2) or 5000 kJ/(mol*nm^2) force constants
> for restraining my protein atoms positions during steepest descent
> minimization
> and as I watch the "trajectory", the atoms of protein still change their
> position.
> The RMSD after 2000 steps is ca. 0.009 nm. Is it something I should expect?

Yes. Restraints disfavor motion, they don't prevent it. 0.009 nm is 
effectively zero.


> I am 100 % sure I correctly apply position restraints as the minimize.trp
> file contains information about them.
> I cannot to conjugate gradient as I keep on getting fatal errors due to
> unsettled water molecules.
> Best wishes,
> Dawid Grabarek


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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