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

Dawid das addiw7 at googlemail.com
Thu Mar 15 16:56:03 CET 2018

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
and as I watch the "trajectory", the atoms of protein still change their
The RMSD after 2000 steps is ca. 0.009 nm. Is it something I should expect?

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

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