<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;">
<br>
<br>
sa wrote:<br>
><br>
> 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>
><br>
><br>
> Yes I have read the help of the tool but it is not clear to me why i<br>
> have to choose three groups since i want to compute the water density<br>
> map around my peptides (-> two groups)<br>
><br>
><br>
<br>
The first two groups determine the axis. Per g_densmap -h:<br>
<br>
"Three groups should be supplied, the centers of mass of the first two<br>
groups define the axis, the third defines the analysis group."<br>
<br>
I suspect the fact that you've chosen "SOL" for the second group might be<br>
causing problems (since, presumably, you have water all around), but I have<br>
never used g_densmap, so I don't know for sure.<br>
<br>
-Justin<br></blockquote><div><br>Ok I will try and play with the different groups of my system to see if it works...<br><br>Stefane<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>
><br>
><br>
> I don't understand your response since with the above command and -o<br>
> argument show that an xpm with the name "6_Peptide_53A6_densmap.xpm"<br>
> 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" target="_blank">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<br>
> 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<br>
> file<br>
><br>
><br>
> Stefane<br>
><br>
><br>
><br>
> Mark<br>
><br>
><br>
><br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
<font color="#888888"><br>
</font></blockquote></div><br>