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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
