[gmx-users] Issue with PMF

[Justin Lemkul]

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?

> 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
> %----------------------------------------------------------
>
> 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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