[gmx-users] help with wham analysis

[Srinivasa Ramisetti]

Dear Gromacs users,

I used gmx wham to obtain the "profile.xvg" with PMF. However, I see 
that all the values in the second column (Energy) in the profile.xvg are 
zeroes. Can someone please explain what could cause this?

I am using the below lines for the pull code inside the mdp file for the 
first reaction coordinate. The pull_coord1_init is spaced at 0.1nm.

; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = SUR
pull_group2_name        = TIP
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_rate        = 0.0           ; 0.01 nm per ps = 10 nm per ns
pull_coord1_init        = .1           ; 0.01 nm per ps = 10 nm per ns
pull_coord1_start       = no           ; define initial COM distance > 0
;pull-print-reference   = yes

Thank you,

Srinivasa