<div>Thanks lot. Happy Thanksgiving!. </div>
<div>-Xianghong Qi<br><br></div>
<div class="gmail_quote">On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni <span dir="ltr"><<a href="mailto:alessandro.casoni@unimi.it">alessandro.casoni@unimi.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Tsjerk Wassenaar ha scritto:
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>Can't help you with VMD, but I do have a script to take care of this in Pymol.<br><br>Cheers,<br>
<br>Tsjerk<br><br>On 11/25/08, xianghong qi <<a href="mailto:xianghong001@gmail.com" target="_blank">xianghong001@gmail.com</a>> wrote:<br> <br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all:<br><br>I am trying to show the dodecahedron box only in vmd since my simulation box<br>is dodecahedron. If I include water, I can see the box is dodecahedron. But<br>
I want to get rid off all of water, then my box will not appear there. How<br>can I keep the dodecahedron box boundaries and solute only? Looks like only<br>the rectangular box boundaries can be drawn in VMD.<br> Does anyone has some suggestions? Appreciate your great help.<br>
Happy Thanksgiving.<br>-Xianghong Qi<br><br>--<br>Some people make the world more special just by being in it.<br><br>_______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read<br>
<a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br> <br></blockquote><br><br> <br></blockquote></div>Hi,<br>you can try this:<br><br>trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact*<br>
<br>or<br><br>trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1<br><br>well...the first converts all your trajectory and the last command extracts 1 frame in a gro file..<br><br>good luck<br><font color="#888888">alessandro</font>
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<div class="Wj3C7c"><br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Some people make the world more special just by being in it.<br>