[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 13:04:28 CEST 2010
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?
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
>>>>
>>>
>
>
--
Dr Thomas Piggot
University of Southampton, UK.
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