[gmx-users] Zero Potential of Mean Force with g_wham

[Jianguo Li]

I met the same problem when using 4.5.1 for some systems, the PMF shows zero 
curve, while the hist file looks fine. The problem disappears when using 4.5.2.
Jianguo




________________________________
From: Susana Tomasio <susietomasio at gmail.com>
To: gmx-users at gromacs.org
Sent: Wednesday, 9 March 2011 20:07:25
Subject: [gmx-users] Zero Potential of Mean Force with g_wham

Dear all,

I am running umbrella sampling of a molecule through a lipid bilayer with 
gromacs 4.5.1.
When I extracted the potential of mean force with g_wham I got zero for all the 
windows.
Any ideas of why this is happening?

This is the command I used: 
g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist

And this is the pull code of my .mdp file:

; Pull code
pull                =  umbrella 
pull_geometry       =  position 
pull_dim            =  N N Y    
pull_start          =  yes      
pull_ngroups        =  1      
pull_group0         =  Bilayer 
pull_group1         =  Protein    
pull_vec1           =  0 0 0    
pull_init1          =  0 0 0   
pull_rate1          =  0       
pull_pbcatom0       =  1453   
pull_pbcatom1       =  13187   
pull_k1             =  3000     ;  kJ mol^-1 nm^-2
pull_nstxout        =  1000     ; every 2 ps
pull_nstfout        =  1000     ; every 2 ps

Thank you.
Best regards,

Susana


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