[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 12:48:57 CEST 2010

Thomas Piggot wrote:
> 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 mistake.
> 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 be.
Ah thanks. I'll correct that soon.

> 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
Ok, I guess I never checked that case. But as you point out, you don't 
have to use -noauto when providing min and max, the auto is switched off 

Thanks for the feedback,


> 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.
> Cheers
> Tom
> 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. 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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