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

Jochen Hub jochen at xray.bmc.uu.se
Wed May 5 11:46:15 CEST 2010

Thomas Piggot wrote:
> Hi,
> 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
Hi Tom,

if you want to distinguish between above and below, 
pull_geometry=position would have been your choice. What I would do now 
is to run g_wham twice with only the histograms from below and a second 
time only with the histograms from above your reference. YOu'll have to 
make appropriate tpr-files.dat and pullx-files.dat input files. Note 
however, that the PMF very close to your reference will be ill-defined 
since the pull code checked the distance to the reference and not the 
z-coordinate. Therefore I would remove simulations in which the ion was 
sometimes above and sometimes below the reference.

To ge the full PMF along the z-axis (which is what you probably want) 
you'll have to do the simulation again (with pull_geometry=position) I'm 

I hope this helps,


> 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.
> Cheers
> Tom

Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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