[gmx-users] Umbrella sampling - regd

ramesh cheerla rameshgromacs at gmail.com
Mon Nov 26 07:03:39 CET 2012

Dear Gromacs users,

     I am calculating  PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations have pullaed pulled the adjacent ions to the vacant binding
site (tunnel is aligned along  Y- axis).
for this I have used the following options in .mdp file.
   ; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N Y N
pull_start      = yes
pull_ngroups    = 1
pull_group0     = REFA
pull_rate1      = 0.01
pull_k1         = 3000      ; kJ mol^-1 nm^-2

Here  pull_group0 = REFA is the ion at another binding site and
pull_group1     = ATBP  is the atom  that I am pulling to the vacant site.
In next step I have performed umbrella sampling simulations to the selected
configurations using the following options :
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N Y N
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = REFA
pull_group1     = ATBP
pull_init1      = 0
pull_rate1      = 0.0      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 3000      ; kJ mol^-1 nm^-2
pull_nstxout    = 100
pull_nstfout    = 100
After that I have constructed PMF profile using Gromacs tool "g_wham",
while using g_wham I am getting the following warnings,
"WARNING, no data point in bin 34 (z=0.889382) !
You may not get a reasonable profile. Check your histograms!"
I have checked my histograms instead of one histogram for each
configuration with perfect overlapping, I am getting only one histogram.
Here I am sending the link that containing PMF profile and histogram that
have obtained.

the weired thing that I have observed in my pulling simulations is that I
have expected motion of ion in positive Y-direction for my pull parameters
but it is moving in negative Y- direction.
 Can anybody please suggest me a solution for this,  Am I following correct
protocol to get PMF of my system, is there any better method that suits for
my system.

Thank you in advance.


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