Re: [gmx-users] extra factor in PMF

2012-04-25 Thread Martin Hoefling
The factor depends on the choice of your reaction coordinate, and since g_wham doesn't care about it - it's not included. It accounts for the change in volume when going from cartesian to general coordinates and can be computed as -k_B * T * (d ln ( | J |) / d_lambda), where lambda is the functio

[gmx-users] extra factor in PMF

2012-04-20 Thread Thomas Schlesier
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)

[gmx-users] extra factor in PMF

2012-04-19 Thread Gavin Melaugh
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