<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><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
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_(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">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></font></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><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; ">"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; 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; ">" 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 </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; ">could anyone helpme in this regard how to do the same analysis in gromacs.</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; ">Thanks in advance </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; ">E R Azhagiya singam </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></div></div><div style="position:
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