[gmx-users] Question about gmx_wham

[Alexander Phillips]

Hi John,

I am trying to determine the binding energy of Vitamin E to various lipid
membranes by pulling it vertically out of the membrane and performing
umbrella sampling during this process.

There are three .mdp files I have but most of them use very similar pull
code, I will differentiate them by slashes
pull-rate1 = A / B / C
Where A B C are the three files
The first file is what I used to initially pull the Vitamin E, the second
file is the npt equilibration that Justin used, and the third is the
production run for umbrella sampling (that justin also used).

The pull code is as follows:

; Pull Code
pull = umbrella
pull-geometry = direction-periodic
pull-start = yes
pull-nstxout = 10
pull-nstfout = 10
pull-ngroups = 1
pull-group0 = Lipids
pull-group1 = PULLING_ATOC
pull-vec1 = 0 0 1
pull-rate1 = 0.00025     /      0     /     0
pull-k1 = 10

The only difference is that I disable the pull rate in the last two of the
three.



Also I installed grace and graphed it just fine, thanks!
Thank you for the paper about gmx_wham that will be very helpful moving
forward,

Alex

On Mon, 14 Oct 2019 at 11:27, John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> Hi,
>
> > Hello,
> >
> > I am currently running Umbrella Sampling simulations on Vitamin E (in
> > grommacs version 4.6.5). And I followed the tutorial done by Justin A.
> > Lemkul, however I am uncertain of a few things about the gmx_wham command
> > that he instructs us to use.
> >
> > Namely for the two output files, which by default are 'profile.xvg' and
> > 'histo.xvg'.
> > I was wondering for the profile.xvg file what does the X-axis refer to,
> as
> > it says 'z' in the output file however is that in Angstroms, Nanometers,
> > etc.
> > The graph I have goes to a value that doesn't make sense in context of my
> > simulation (goes to a Z of 70 towards the end which is larger than the
> > Z-axis of my simulation  if it was in Angstroms (did it account for
> > periodic boundary conditions?)).
>
> The x-axis of profile.xvg is whatever the reaction coordinate was for your
> umbrella sampling simulations. The reaction coordinate will change
> depending on what system you have and what you're trying to calculate. For
> example, in Justin's tutorial the reaction coordinate is the z-axis and
> what is outputted (in pullx.xvg) is the distance between the protofibril
> and "peptide A" calculated only in the z direction.
>
> You should post the pulling parameters from your .mdp file and describe
> what you're trying to learn about your system by doing umbrella sampling.
> Otherwise, it's hard to help.
>
> > Secondly I was wondering how to graph the histo.xvg file as I was having
> > issues using GNUPLOT, if I shouldn't use GNUPLOT what different graphing
> > program should I use?
>
> histo.xvg has many columns, not just 2 like you have from something like a
> pullx.xvg file. You're probably not plotting all the columns, but I'm not
> sure because you didn't specify what issue you're having.
>
> To get a quick idea of whether or not my histograms are overlapping, I
> normally just use Grace with a command like:
>
> xmgrace -nxy histo.xvg
>
> -nxy tells Grace to assume the data file is in X Y1 Y2 Y3 ... format so it
> plots all your histograms.
>
>
> > If there are pages where this information is readily available, please
> let
> > me know and I will use them, however I could not find them so I would
> like
> > your help.
> >
>
> maybe the gmx wham paper will be useful:
>
> http://cmb.bio.uni-goettingen.de/pub/Hub_JCTC2010.pdf
>
>
> > Thank You,
> > Alex
> > --
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>
> - John
>
>
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