<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Pymol has similar functionality, in case you prefer that over VMD.<div><br><div><div>5 jun 2012 kl. 22.23 skrev Peter C. Lai:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>You can also use something like VMD where you load the trajectory then <br>select your atoms, then increment the frames and extract the xyz coordinates<br>of each of your atoms in the selection. You can do that in 5 lines of TCL<br>script (just don't update the select within selection after each frame or<br>else it will reselect a new set of molecules based on the distance criteria,<br>if you're trying to track the same water molecules from beginning to end).<br><br>On 2012-06-05 06:02:22AM -0700, rankinb wrote:<br><blockquote type="cite">I am interested in pulling out the trajectories (x,y,z coordinates) of water<br></blockquote><blockquote type="cite">molecules within a certain distance of my solute molecule. I have tried<br></blockquote><blockquote type="cite">using g_select, but that will only give me the atom numbers and not the<br></blockquote><blockquote type="cite">trajectories. I can create an index file using this command but<br></blockquote><blockquote type="cite">unfortunately each time frame is set as a different group. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is there a way to get the trajectories at all frames of only the water<br></blockquote><blockquote type="cite">molecules within a specified distance of a solute molecule? <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you very much,<br></blockquote><blockquote type="cite">Blake<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">View this message in context: <a href="http://gromacs.5086.n6.nabble.com/Trajectories-tp4998094.html">http://gromacs.5086.n6.nabble.com/Trajectories-tp4998094.html</a><br></blockquote><blockquote type="cite">Sent from the GROMACS Users Forum mailing list archive at <a href="http://Nabble.com">Nabble.com</a>.<br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the <br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote><br>-- <br>==================================================================<br>Peter C. Lai<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>| University of Alabama-Birmingham<br>Programmer/Analyst<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>| KAUL 752A<br>Genetics, Div. of Research<span class="Apple-tab-span" style="white-space:pre"> </span>| 705 South 20th Street<br><a href="mailto:pcl@uab.edu">pcl@uab.edu</a><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>| Birmingham AL 35294-4461<br>(205) 690-0808<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>|<br>==================================================================<br><br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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