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

Thomas Piggot t.piggot at soton.ac.uk
Wed May 5 12:12:13 CEST 2010

Jochen thanks for your help.

That was what I was afraid of you saying. Oh well, at least this will 
hopefully provide a useful reference so somebody doesn't make this same 

On a side note I noticed a couple of small issues with g_wham. Firstly 
the -wcorr option says Input, opt. not Output, opt as I assume it should 

Also when using -min and -max with the -noauto option, the program quits 
with the error:

Fatal error:
With -auto, do not give -min or -max

This is not a problem as with -min and -max (without specifying -noauto) 
g_wham switches automatically switches auto off, but I assumed that 
using -min and -max the -noauto option would have been the 'correct' way 
to do this.



Jochen Hub wrote:
> 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 
> afraid.
> I hope this helps,
> Jochen
>> 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 Thomas Piggot
University of Southampton, UK.

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