[gmx-users] UMBRELLA SAMPLING

[Erik Marklund]

It's just the xvv file. g_wham uses the letter 'z' to denote the reaction coordinate.

Erik

On 2 Jul 2013, at 11:32, battistia at libero.it wrote:

> 
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> 
> 
> 
> 
> 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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