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

[Jochen Hub]

Thomas Piggot wrote:
> Hi again,
>
> Just before I reside myself to rerunning a large number of simulations 
> I was wondering if it is possible to just rerun the simulations where 
> the ion is above and below the reference using pull_geometry=position. 
> Then could I combine these with the other simulations where 
> pull_geometry=distance to get the complete PMF?
Hm,

that may get tricky but may be possible. g_wham can probably not deal 
with it when you use the -it and -ix input (with 2 different pulling 
geometries). But you could turn the pullx files into pdo files (check 
g_wham -h) to provide them with -ip to g_wham. That will certainly 
require a bit of scripting, but should not be too difficult. Make sure 
to get the direction (plus/minus z) right when turning the distance in 
the pullx into pdo files with z as reaction coordinate.

Good luck,

Jochen
>
> Tom
>
> Jochen Hub wrote:
>> 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 automatically.
>>
>> Thanks for the feedback,
>>
>> Jochen
>>
>>> 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
>>>>>
>>>>
>>
>>
>


-- 
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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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