[gmx-users] problem calculating PMF with distant constraints
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 15 20:31:56 CET 2005
rzangi at att.net wrote:
> 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.
the dHdl curve is meaningless, only the integral is physcially
meaningfull. Of course you can compare to other simulations done in an
> 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?
I don't know what to do about this, there definitely is no standard
> 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 ?
I'm not completely sure that you used the right method. If you put a
constraint between the atoms they won't interact at all, unless you set
nrexcl to zero. An alternative method is to freeze the Neon atoms and
measure the force on them.
> 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.
If you have a well defined system where you think you are doing exactly
the same as in a publication, and you still can not reproduce it then
feel free to post a bug report on bugzilla.gromacs.org. I assume you are
reasonably sure that your reference values are correct.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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