Hi,

We have studied a small 4-residue protein with CHARMM's

parameter set 22 (with CMAP correction terms) in explicit

TIP3 water (constant pressure & temperature), SHAKE on

hydrogen bonds, 2fs time-step (leap frog).

We note that the average bond lengths are all slightly

above their equilibrium value of the harmonic potential.

For example, the N-terminal bond +H3N---C(alpha) of the

first residue (Gly) has an average value of 1.50 Ang;

whereas the equilibrium bond length of the CHARMM potential

is 1.48 Ang in the parameter set 22.

When we construct from the trajectory the potential of

mean force we obtain a harmonic potential that is

slightly shifted to larger values, and the force

constant is also slightly increased (250 kcal mol-1 Ang-2

instead of 200 kcal mol-1 Ang-2 of the CHARMM potential).

This is not due to statistical errors as you can see by

the error bars; the bars correspond to the standard

deviation for five independent runs (each them 1.5 microseconds long!).

What could be the reason for this increase in

the equilibrium distance and the force constant?

Is this a general behavior?

Thanks,

Martin