[gmx-users] Re: gmx-users Digest, Vol 79, Issue 88

[sa]

> On 13/11/2010 4:07 AM, sa wrote:
> > Dear All,
> >
> > I would like to compute the average 2D density distribution of the
> > water around 6 peptides aggregated in the cluster within the
> > simulation box with gromacs, for that I think that g_densmap is the
> > the good tool (correct ?).
> >
> > However it is not very clear for how to use g_densmap. Below the
> > command I used with g_densmap (ver GMX 4.5.3)
> >
> > g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s
> > ./TRAJ/TPR/em.tpr  -bin 0.02 -amax 30 -rmax 30 -b 0 -e 80000 -o
> > 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat
> >
> > When I use the above command, g_densmap asks me to choose two groups
> > to define the axis and an analysis group:
> >
> > Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)
> > Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)
> > Select two groups to define the axis and an analysis group
> > Group     0 (         System) has 86359 elements
> > Group     1 (        Protein) has   546 elements
> > Group     2 (      Protein-H) has   396 elements
> > Group     3 (        C-alpha) has    48 elements
> > Group     4 (       Backbone) has   144 elements
> > Group     5 (      MainChain) has   192 elements
> > Group     6 (   MainChain+Cb) has   234 elements
> > Group     7 (    MainChain+H) has   246 elements
> > Group     8 (      SideChain) has   300 elements
> > Group     9 (    SideChain-H) has   204 elements
> > Group    10 (    Prot-Masses) has   546 elements
> > Group    11 (    non-Protein) has 85813 elements
> > Group    12 (          Other) has 17320 elements
> > Group    13 (            URE) has 17320 elements
> > Group    14 (             CL) has     6 elements
> > Group    15 (          Water) has 68487 elements
> > Group    16 (            SOL) has 68487 elements
> > Group    17 (      non-Water) has 17872 elements
> > Group    18 (            Ion) has     6 elements
> > Group    19 (            URE) has 17320 elements
> > Group    20 (             CL) has     6 elements
> > Group    21 ( Water_and_ions) has 68493 elements
> > Select a group: 1
> > Selected 1: 'Protein'
> > Select a group: 16
> > Selected 16: 'SOL'
> > Select a group: 16
> > Selected 16: 'SOL'
> >
> > I chose protein and SOL, the program ask me to choose a third group
> > (?) What to choose ?
>
> Doesn't g_densmap -h explain the three groups?
>

 Yes I have read the help of the tool but it is not clear to me why i have
to choose three groups since i want to compute the water density map around
my peptides (-> two groups)

>
> > I choose SOL again, the program computes something but i can not
> > inspect the results are what i want since no xpm is generated by
> > g_densmap (is this a bug ?)
>
> Probably badly-formed input is silently breaking something somewhere.
>

I don't understand your response since with the above command and -o
argument show that an xpm with the name "6_Peptide_53A6_densmap.xpm" should
appear


                         :-)  G  R  O  M  A  C  S  (-:

                     Gnomes, ROck Monsters And Chili Sauce

                            :-)  VERSION 4.5.3  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

           :-)  /work/taulier01/gromacs-4.5.3/bin/g_densmap_mpi  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc  Input        Trajectory: xtc trr
trj
                                   gro g96 pdb cpt
  -s ./TRAJ/TPR/em.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
                                   pdb
  -n      index.ndx  Input, Opt.  Index file
 -od 6_Peptide_53A6_densmap.dat  Output, Opt! Generic data file
  -o 6_Peptide_53A6_densmap.xpm  Output       X PixMap compatible matrix
file


Stefane



> Mark
>
>
>
>
>
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