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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"
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          <div style="color: black; font-family: 'times new roman','new
            york',times,serif; font-size: 12pt;">Dear all&nbsp;</div>
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            york',times,serif; font-size: 12pt;">"<a
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href="http://www.sciencedirect.com/science?_ob=MImg&amp;_imagekey=B94RW-4TYB1FX-K-1&amp;_cdi=56421&amp;_user=1245000&amp;_pii=S0006349500765337&amp;_coverDate=12/31/2000&amp;_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&amp;view=c&amp;_gw=y&amp;wchp=dGLbVlb-zSkWb&amp;md5=4e66a17da4627571bfd990beae45d486&amp;ie=/sdarticle.pdf">http://www.sciencedirect.com/science?_ob=MImg&amp;_imagekey=B94RW-4TYB1FX-K-1&amp;_cdi=56421&amp;_user=1245000&amp;_pii=S0006349500765337&amp;_coverDate=12/31/2000&amp;_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&amp;view=c&amp;_gw=y&amp;wchp=dGLbVlb-zSkWb&amp;md5=4e66a17da4627571bfd990beae45d486&amp;ie=/sdarticle.pdf</a>"</div>
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          <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 &nbsp;hydration map it
              says&nbsp;</font></div>
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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,&nbsp;the protein was fitted to a consistent frame
            of reference."&nbsp;</div>
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          <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>
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          <div style="color: black; font-family: 'times new roman','new
            york',times,serif; font-size: 12pt;">" Next, the same
            &nbsp;transformation was applied to the water molecule
            coordinates, taking the&nbsp;periodic boundaries into account."</div>
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          <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>
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            " The coordinates of the water oxygen &nbsp;atoms were then
            mapped onto the three-dimensional rectangular grid with&nbsp;a
            0.5 &Aring; grid step, producing an average three-dimensional
            number density&nbsp;distribution. The particular choice of the
            grid step is a compromise between&nbsp;the uncertainty in
            location of the density features and the statistical error
            in&nbsp;the local density value that arises due to a lower number
            of counts in each &nbsp;grid cell.&nbsp;At the chosen grid step every
            cell in the regions corresponding to&nbsp;bulk solvent would have
            at least 50 counts over the entire trajectory. The&nbsp;density
            map was smoothed by averaging the value of each cell with
            six of&nbsp;its nearest neighbors before further manipulations.&nbsp;"</div>
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          <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>
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          <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 &nbsp;given in the above mentioned paper <br>
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    </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"
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          <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>
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    </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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