[gmx-users] Re: gmx-users Digest, Vol 99, Issue 12

Thomas Schlesier schlesi at uni-mainz.de
Tue Jul 3 21:30:25 CEST 2012

ok, had still the 4.0.x version in mind, there the .tpr-files were not used.
could be that the factor was introduced in 4.5.x, but i don't think so.

If there would be steric crashes, which would account for the strong 
increase in the PMF, one should see them in the force profile.

for more information on the factor in regard to TI:
E. Paci, G. Ciccotti, M. Ferrario; Chem. Phys. Letters 176, 6: 581-587, 1991

On 7/3/12 2:50 PM, Thomas Schlesier wrote:
 > think you encounter the problem, that you construct your pmf from a 3d
 > simulation and project it onto 1d, but do no correction.
 > For TI (if you constrain the distance in all three directions) the 
pmf is given by
 > V_pmf(r) = - \int [ F_c + 2/(beta*r) ] dr
 > with F_c the constraint force and \beta = 1/(k_B*T).
 > for umbrella sampling one should need the same factor
 > -2/beta \int 1/r dr
 > if one restraints the system in 3 directions.
 > Since 'g_wham' uses no *.tpr it can not know the value of 'pull_dim' 
one should
 > introduce the factor afterwards.

The input to g_wham (at least in modern Gromacs versions) is a list of .tpr
files (passed to the -it flag) and a list of pullx or pullf files (with 
-ix or
-if).  How is g_wham ignorant of these pull settings?


More information about the gromacs.org_gmx-users mailing list