Thanks Justin for the response. On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.