> > > 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 > > ======================================== > > > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists