[gmx-users] Issue with PMF

[Alex]

Thanks Justin for the response.

On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/2/20 12:53 PM, Alex wrote:
> > Dear all,
> > By using the below setting I am getting a very nice umbrella histogram
> and
> > iact also shows a very good integrated Autocorrelation time. However, the
> > PMF profile is unexpected. Below I have also provided a gmx wham command
> I
> > am using, part of the pullx.xvg of one of the windows and also
> > corresponding part in log file.
> > Would you please help me find out what the problem might be?
>
> What is the problem?
>
Below link shows the histogram and PMF, actually I was expecting that the
PMF reach a plateau in the region marked by B in the figure as we are fully
inside the bulk area of the thin film. However, there are some region from
15 to 20 kcal/mol different respect to the expected plateau. Here we have
10nm thick thin film.

https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz


> > One more question: does it make sense to manually shift the plateau of
> the
> > PMF plot to zero (when we plot it), instead of using using the -zprof0
> flag?
>
> There is no difference. The -zprof0 just adds a constant so the PMF is
> zero at the specified point on the reaction coordinate.
>
> > %--------------------------------
> > pull                     = yes
> > pull-ngroups             = 2
> > pull-ncoords             = 1
> > pull-group1-name         = Mol_A
> > pull-group2-name         = Thin_film
> >
> > pull-coord1-groups       = 1 2
> > pull-coord1-type         = umbrella
> > pull-coord1-dim          = N N Y
> > pull-coord1-start        = no   ;--> manually we define the distance for
> > all windows
> > pull-coord1-rate         = 0.0  ;--> We don't want the roups to move
> > pull-coord1-geometry     = distance
> > pull-coord1-k            = 10000   ;;kJ/(mol nm^2)
> > pull-print-components    = Yes
> > pull-nstxout             = 2000
> > pull-nstfout             = 2000
> > pull-print-com1          = yes
> > pull-coord1-init         = 1.650000
> > %------------------------------------
> > #Part of the one of the pullx.xvg file
> > @ legend length 2
> > @ s0 legend "1"
> > @ s1 legend "1 dZ"
> > @ s2 legend "1 g 1 Z"
> > @ s3 legend "1 g 2 Z"
> > 0.0000  0.0155171       0.0155171       9.89805 9.91357
> > 2.0000  0.0103956       0.0103956       9.90227 9.91266
> > 4.0000  0.0146962       0.0146962       9.89733 9.91202
> > 6.0000  0.00656533      0.00656533      9.90404 9.91061
> > 8.0000  0.00228074      0.00228074      9.90945 9.91174
> > 10.0000 0.00967605      0.00967605      9.90514 9.91482
> > ....
> > %--------------------------------------------
> > gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist
> > -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o
> > profile.xvg -b 3000 -unit kCal -v
> >
> >   %------------------------------------------------
> > #Similar massage as below I have for all windows (tpr files).
> > Reading file prd.1.tpr, VERSION 2018.7 (single precision)
> >
> > File prd.1.tpr, 1 coordinates, with these options:
> >          Geometry distance   k = 10000     position = 0
>  dimensions
> > [N N Y] (1 dimensions). Used: Yes
> >          Pull group coordinates of 2 groups expected in pullx files.
> >          Reference value of the coordinate not expected in pullx files.
> >
> > Reading pull force file prd_pullf.1.xvg, expecting 2 columns:
> >          Columns for pull coordinate 1
> >                  reaction coordinate:             1
> >                  center-of-mass of groups:        0
> >                  reference position column:       No
> >          Found 2501 times in prd_pullf.1.xvg
> > %----------------------------------------------------------
>
Actually, I was suspicious of these "Reference value of the coordinate not
expected in pullx files."  and "reference position column:       No" which
I have in log file of gmx wham for each windows's tpr.

Concerning your PMF tutorial, when the distance between chain_A and chain_B
is calculated by gmx distance, why the -oall is used to get the absolute
distance out of x,y and z, while the -oxyz would be much better as we can
take the Z component of the distance similar (corresponding) to the
considered reaction coordinate in the tutorial?

Regards,
Alex

> >
> > Thank you,
> > Alex
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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