[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel
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:
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:
>> 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
>> 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.
Dr Thomas Piggot
University of Southampton, UK.
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