[gmx-users] gromacs

battistia at libero.it battistia at libero.it
Tue Jul 2 11:31:19 CEST 2013

Dear users and experts

I'm doing an umbrella-samplig calculation to obtain the PMF when two structure (A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:

; Pull type: no, umbrella, constraint or constant_force
pull                     = umbrella
pull_geometry            = distance
pull_dim                 = Y N N
pull_start               = yes
pull_nstxout             = 1000
pull_nstfout             = 1000
; Number of pull groups
pull_ngroups             = 1
pull_group0              = A
pull_group1              = B
pull_init1               = 0
pull_rate1               = 0.0
pull_k1                  = 1000
pull_kB1                 = 1000

but when I run the program g_wham:

g_wham -it tpr-files.dat -if pullf-files.dat -o profile.xvg -hist histo.xvg

the profile I obtain is respect to the z coordinate (PMF as a function of z).

My question is:  is this only a problem of xvg text, or the PMF is effectively calculated with respect to the z variable, although I selected

pull_dim = Y N N?

Thank you very much


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