[gmx-users] problem calculating PMF with distant constraints

rzangi at att.net rzangi at att.net
Thu Dec 15 20:12:16 CET 2005

I am trying to calculate potential of mean force between two atoms (neon, methane) by running multiples simulations with distances that are constrained from lambda=0 to lambda=1 and then integrating <dHdl>. However, this doesn't seem to give the right curve as compare to calculations obtained with other methods. There appears to be a serious discrepancy.

In particular when the constraint distance was bigger than the cut-off interaction (so the two atoms don't `see' each other) and bigger than the range of the solvent induced interactions, the constraint force was not zero but replusive. This can be related to what was mentioned in the literature before [Chem. Phys. Lett. 196 297 (1992), JCP 100 9129(1994)] as a `dynamic' contribution to the free energy when the system allowed to rotate (the centripetal force). Thus, even when there are no forces on the atoms, but ones allow distance constraint to rotate the atoms will experience a force in the opposite direction to their center of mass, which, of course, should not be in the PMF - is there such correction to this in Gromacs?

Nevertheless, if one restrains the two atoms from moving along the x and y axis and sets the constraint distance along the z-axis it still doesn't give the right answer.

Did someone reported these issuses before                                                                             ?

This was checked with 3.2.1 and 3.1.4 versions, with a few different water
models, PME and cut-offs for the electrostatic interactions as well.

Is there a simple fix? The group I am working in is quite concerned about this.



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