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On 13/11/2010 6:07 PM, babu gokul wrote:
<blockquote cite="mid:174026.66900.qm@web95313.mail.in2.yahoo.com"
type="cite">
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<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">Dear all </div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">"<a
moz-do-not-send="true"
href="http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4TYB1FX-K-1&_cdi=56421&_user=1245000&_pii=S0006349500765337&_coverDate=12/31/2000&_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_%28December_2000%29%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23%28December_2000%29%23&view=c&_gw=y&wchp=dGLbVlb-zSkWb&md5=4e66a17da4627571bfd990beae45d486&ie=/sdarticle.pdf">http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4TYB1FX-K-1&_cdi=56421&_user=1245000&_pii=S0006349500765337&_coverDate=12/31/2000&_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_(December_2000)%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23(December_2000)%23&view=c&_gw=y&wchp=dGLbVlb-zSkWb&md5=4e66a17da4627571bfd990beae45d486&ie=/sdarticle.pdf</a>"</div>
<div><f ont="" class="Apple-style-span" face="'times new
roman', 'new york', times, serif"><br>
</f></div>
<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif">I read the above linked paper
about the to find a molecular density hydration map it
says </font></div>
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york',times,serif; font-size: 12pt;"><br>
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<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">"For each step of the
MD trajectory, the protein was fitted to a consistent frame
of reference." </div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">I did this by using
trjconv i have fitted the protein in my trajectory</div>
<div style="color: black;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">" Next, the same
transformation was applied to the water molecule
coordinates, taking the periodic boundaries into account."</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">I did the same by using
trjconv by using the trajectory i have obtained from the
previous step</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
" The coordinates of the water oxygen atoms were then
mapped onto the three-dimensional rectangular grid with a
0.5 Å grid step, producing an average three-dimensional
number density distribution. The particular choice of the
grid step is a compromise between the uncertainty in
location of the density features and the statistical error
in the local density value that arises due to a lower number
of counts in each grid cell. At the chosen grid step every
cell in the regions corresponding to bulk solvent would have
at least 50 counts over the entire trajectory. The density
map was smoothed by averaging the value of each cell with
six of its nearest neighbors before further manipulations. "</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">I did the above step by
using GridCount tool i got a grid.dat then i transformed the
that to a vmd readable format density map.</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">but when i visualize
the file in vmd i got a lot of density over the corner but i
was not able to visualize the it near the protein molecule
as given in the above mentioned paper <br>
</div>
</div>
</div>
</blockquote>
<br>
The simplest thing that can go wrong is that your visualization of
the density is based on an unsuitable range of density. However,
you'll have to consult the documentation of GridCount and VMD -
you're not very likely to get help for those on a GROMACS mailing
list.<br>
<br>
<blockquote cite="mid:174026.66900.qm@web95313.mail.in2.yahoo.com"
type="cite">
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font-size: 12pt;">
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<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">could anyone helpme in
this regard how to do the same analysis in gromacs.</div>
</div>
</div>
</blockquote>
<br>
g_density can calculate 3D number density histograms, however there
might be a bunch of work to (say) visualize that histogram in (say)
VMD overlaying your system, or such.<br>
<br>
Mark<br>
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