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On 13/11/2010 4:58 AM, sa wrote:
<blockquote
cite="mid:AANLkTikTpC9h=E1-_Vq6=77-36OPzKH7VJve6-MmSA5e@mail.gmail.com"
type="cite"><br>
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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>
</div>
</blockquote>
<br>
You need to define an axis by the line between the centers of mass
of two groups. Almost surely the COM of your protein cluster and the
COM of your water is a random line. I don't know what there is about
your system that makes you want a 2D density distribution, but if
there is, you need to come up with a sensible axis around which to
compute. Only then does the distribution of third group get
computed.<br>
<br>
<blockquote
cite="mid:AANLkTikTpC9h=E1-_Vq6=77-36OPzKH7VJve6-MmSA5e@mail.gmail.com"
type="cite">
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<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>
</div>
</div>
</blockquote>
<br>
Agreed, but lets get your input formed sensibly before deducing that
there's a bug or anything.<br>
<br>
I had a quick look at the code, and Peter Kasson designed it so that
if you use -od then you won't get the -o output. You could get both
from two invocations of g_densmap, which doesn't sound like a good
design, and certainly contradicts the documentation. For the moment,
I'll fix the documentation.<br>
<br>
Mark<br>
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