[gmx-users] Issue with PMF
Quyen V. Vu
vuqv.phys at gmail.com
Sun Apr 5 13:10:01 CEST 2020
Dear Justin,
In your tutorial, you selected the initial configuration for each umbrella
by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)]
and in umbrella sampling simulation, your setting is:
pull_coord1_dim = N N Y
pull_coord1_start = yes
so as the draw I attached here you can see that conf1,conf2 and conf3
are satisfied the distance criteria and you used the staring
z-separation as reaction coordinates, this mean umbrella 1 and 2 will
sample the same region while the region between zeta_1 and zeta_3 is
not sampled well if |zeta3-zeta1| is large.
https://drive.google.com/open?id=1nUKLmaBhjL29ZadgUcPk6DlG08ZVP_Nx
Is it true?
Best regards,
Quyen
On Thu, Apr 2, 2020 at 10:28 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/2/20 4:19 PM, Alex wrote:
> > 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
> >
>
> Bootstrapping may underestimate the real error. How well converged is
> the PMF with respect to time, e.g. computing the PMF from the first half
> and last half of the simulation time?
>
> >>> 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.
>
> I have no experience with that; the pullx.xvg file format has changed a
> lot over time. I always use pullf.xvg and it's never an issue.
>
> > 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?
>
> The two quantities should be essentially equivalent for the purposes of
> the tutorial.
>
> -Justin
>
> > 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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
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>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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