[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot t.piggot at soton.ac.uk
Tue May 4 19:02:16 CEST 2010


I am trying to construct a PMF profile for a phosphate ion passing 
through a membrane protein using umbrella sampling with GROMACS 4.0.5.

I have performed the umbrella sampling simulations using the following 
mdp options and I am now attempting to construct the PMF using g_wham.

; Pull code
pull                =  umbrella ; do umbrella sampling
pull_geometry       =  distance ; can't get PMF with direction
pull_dim            =  N N Y    ; just in the z
pull_start          =  yes      ; add com to pull_init1
pull_ngroups        =  1        ; no. of groups to pull
pull_group0         =  Protein  ; reference group
pull_group1         =  PO4      ; pull group
pull_vec1           =  0 0 0    ;
pull_init1          =  0        ;
pull_rate1          =  0.0      ; no change in ref position
pull_k1             =  1000     ; force constant for restraint
pull_nstxout        =  1000     ; every 2 ps
pull_nstfout        =  1000     ; every 2 ps

The problem is that when running g_wham (using the following command) 
g_wham correctly reads all of the tpr and pullx files, however the data 
for the windows above and below the reference atom (the middle atom of 
the protein) are both included in the same part of the PMF profile.

g_wham_4.0.5 -ix -it -cycl weighted -b 2000

I assume that this is occuring due to the pull_geometry = distance 
option, as the distance to the reference does not matter if the ion is 
above or below the reference?

So my question is: Is there a way to construct the complete PMF profile 
  with the simulations I have already run?

I should also mention that I have tried using the -min and -max options 
with g_wham (rather than the auto determination of the boundaries) but 
this just produces outputs that have all the values as nan. I have also 
tried using g_wham 4.0.7 but with exactly the same issues ,as well as 
using the pullf.xvg files as input to g_wham.

I apologise if I am missing something obvious (or doing something 
silly!) but any help would be greatly appreciated.



Dr Thomas Piggot
University of Southampton, UK.

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