[gmx-users] Re: gmx-users Digest, Vol 79, Issue 89
sa
sagmx.mail at gmail.com
Fri Nov 12 20:17:10 CET 2010
>
>
> 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
>
Ok I will try and play with the different groups of my system to see if it
works...
Stefane
>
> > > 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
>
> ========================================
>
>
>
>
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