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:
; COM PULLING
; 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
Anna
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