AFAIK this factor isn't included in g_wham. Think i tested this some
years ago with an older GROMACS version.
If one looks into the 'gmx_wham.c' and searches for 'ln' one finds it
only in the comments for the gaussian random numbers.
Greetings
Thomas
Hi all
According to some references
1) J. Chem. Phys, 128, 044106, (2008)
2) Comparison of Methods to Compute the Potential of Mean Force
Daniel Trzesniak, Anna-Pitschna E. Kunz, Wilfred F. van Gunsteren Prof.
Article first published online: 28 NOV 2006
DOI: 10.1002/cphc.200600527
There is an extra factor that has to be taken into account when
calculating the PMF. This extra factor (2kTln(r)) results from the
transformation from the 3N Cartesian coordinates to 3N internal
coordinates. In the case of a reaction coordinate defined by a distance
r between two species the Jacobian (r*2sin(theta)) of the transformation
for 3D to 1D leads to an extra term in the PMF.
Therefore the true PMF should be
PMF(true) = PMF(g_wham) + 2kTln(r)
This extra factor is only significant at lower values of the reaction
coordinate. My question is; Does g_wham take this into account ?
Cheers
Gavin
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
