[gmx-users] Equilibration from Non-shifted to Shifted Potential

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 14 15:31:53 CET 2014


Try it and see ;-)

mdrun -nsteps 10 -reprod -deffnm shifted
mdrun -nsteps 10 -reprod -deffnm not-shifted
gmx check -f shifted -f2 not-shifted
gmx check -e shifted -e2 not-shifted

Alternatively, given that the forces are not computed from the energies
(e.g. by central difference or some such), what role does the potential
energy play in the integration scheme? :-)


On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
> If I change my potential from non-shifted to shift, will the sudden change
> of energy from non-shifted to shifted potential at step 0 completely mess
> up the equilibration?
> Thanks again.
> --
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