[gmx-users] g_densmap options and use

[Justin A. Lemkul]

sa wrote:
> 
>     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)
> 
> 

The first two groups determine the axis.  Per g_densmap -h:

"Three groups should be supplied, the centers of mass of the first two
groups define the axis, the third defines the analysis group."

I suspect the fact that you've chosen "SOL" for the second group might be 
causing problems (since, presumably, you have water all around), but I have 
never used g_densmap, so I don't know for sure.

-Justin

>      > 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
> 
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================