Hello,<br><br><b><i>priyanka srivastava <priyankaps4@yahoo.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Dear all,<br><br>I wish to calculate the density profile of a lipid bilayer i.e the electron density and this is how I am using the g_density command:<br><br>g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm<br><br>where electrons.dat contains # of electrons for each and every atomtype defined in the system e.g.<br>C2A = 6<br>NTM = 7<br>OA = 8 etc....<br><br>However it reports electron density for 50bins (setup by -sl) which ranges from 0 to 50. However I want it to vary from, -30 to +30. <br><br></blockquote>Maybe I'm wrong, but it reports the electron density along the z axis of the box with a grid what contains 50 bins. So to get an electron density which ranges from -30 to +30 (in Angstroms and with the bilayer center at 0, I
guess) you should only shift the z values with half of your box size. <br><blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Another point is, I want the density profile separately for P, N, acyl, water etc. Should I define a separate electrons.dat for this purpose? <br></blockquote>No, you should make an index file for that which contains P, N, etc. groups and run g_density -n new_index.ndx ...<br><blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Kindly suggest me as to how should I proceed,<br>eagerly waiting for your reply,<br>Priyanka S...<br><div> </div><hr size="1">Looking for a deal? <a href="http://us.rd.yahoo.com/evt=47094/*http://farechase.yahoo.com/;_ylc=X3oDMTFicDJoNDllBF9TAzk3NDA3NTg5BHBvcwMxMwRzZWMDZ3JvdXBzBHNsawNlbWFpbC1uY20-">Find great prices on flights and hotels</a> with Yahoo!
FareChase._______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br></blockquote>Hope that helped,<br><br>Zoltan Varga<br><p> 
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