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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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