<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On 13/11/2010 4:07 AM, sa wrote:<br>
> Dear All,<br>
><br>
> I would like to compute the average 2D density distribution of the<br>
> water around 6 peptides aggregated in the cluster within the<br>
> simulation box with gromacs, for that I think that g_densmap is the<br>
> the good tool (correct ?).<br>
><br>
> However it is not very clear for how to use g_densmap. Below the<br>
> command I used with g_densmap (ver GMX 4.5.3)<br>
><br>
> g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s<br>
> ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 80000 -o<br>
> 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat<br>
><br>
> When I use the above command, g_densmap asks me to choose two groups<br>
> to define the axis and an analysis group:<br>
><br>
> Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)<br>
> Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)<br>
> Select two groups to define the axis and an analysis group<br>
> Group 0 ( System) has 86359 elements<br>
> Group 1 ( Protein) has 546 elements<br>
> Group 2 ( Protein-H) has 396 elements<br>
> Group 3 ( C-alpha) has 48 elements<br>
> Group 4 ( Backbone) has 144 elements<br>
> Group 5 ( MainChain) has 192 elements<br>
> Group 6 ( MainChain+Cb) has 234 elements<br>
> Group 7 ( MainChain+H) has 246 elements<br>
> Group 8 ( SideChain) has 300 elements<br>
> Group 9 ( SideChain-H) has 204 elements<br>
> Group 10 ( Prot-Masses) has 546 elements<br>
> Group 11 ( non-Protein) has 85813 elements<br>
> Group 12 ( Other) has 17320 elements<br>
> Group 13 ( URE) has 17320 elements<br>
> Group 14 ( CL) has 6 elements<br>
> Group 15 ( Water) has 68487 elements<br>
> Group 16 ( SOL) has 68487 elements<br>
> Group 17 ( non-Water) has 17872 elements<br>
> Group 18 ( Ion) has 6 elements<br>
> Group 19 ( URE) has 17320 elements<br>
> Group 20 ( CL) has 6 elements<br>
> Group 21 ( Water_and_ions) has 68493 elements<br>
> Select a group: 1<br>
> Selected 1: 'Protein'<br>
> Select a group: 16<br>
> Selected 16: 'SOL'<br>
> Select a group: 16<br>
> Selected 16: 'SOL'<br>
><br>
> I chose protein and SOL, the program ask me to choose a third group<br>
> (?) What to choose ?<br>
<br>
Doesn't g_densmap -h explain the three groups?<br></blockquote><div><br> 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) <br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
> I choose SOL again, the program computes something but i can not<br>
> inspect the results are what i want since no xpm is generated by<br>
> g_densmap (is this a bug ?)<br>
<br>
Probably badly-formed input is silently breaking something somewhere.<br></blockquote><div><br>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<br>
<br><br> :-) G R O M A C S (-:<br><br> Gnomes, ROck Monsters And Chili Sauce<br><br> :-) VERSION 4.5.3 (-:<br><br> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<br>
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<br> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,<br> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,<br>
Michael Shirts, Alfons Sijbers, Peter Tieleman,<br><br> Berk Hess, David van der Spoel, and Erik Lindahl.<br><br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2010, The GROMACS development team at<br>
Uppsala University & The Royal Institute of Technology, Sweden.<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) /work/taulier01/gromacs-4.5.3/bin/g_densmap_mpi (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc Input Trajectory: xtc trr trj<br>
gro g96 pdb cpt<br> -s ./TRAJ/TPR/em.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96<br> pdb<br> -n index.ndx Input, Opt. Index file<br>
-od 6_Peptide_53A6_densmap.dat Output, Opt! Generic data file<br> -o 6_Peptide_53A6_densmap.xpm Output X PixMap compatible matrix file<br><br><br>Stefane<br><br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Mark<br>
<br>
<br>
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