<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>5 jun 2012 kl. 15.05 skrev Justin A. Lemkul:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br><br>On 6/5/12 9:02 AM, 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><br>At present, there is no elegant way to construct such a trajectory, since, in principle, each frame can have a different number of atoms based on which water molecules satisfy the given criteria. Each index group that g_select provides corresponds to an individual frame in the original trajectory, which you can use to pull out individual coordinate files. Perhaps a multi-frame .pdb or .gro file would work, but I believe that .xtc and .trr files have to have the same number of atoms in each frame to be interpreted correctly.<br><br>-Justin<br></div></blockquote><div><br></div><div>g_order orders the molecules according to distance to solute. Then you can pick out the N first from each frame. It is, however, a bit cumbersome for an entire trajectory.</div><div><br></div><div>Erik</div><br><blockquote type="cite"><div><br>-- <br>========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><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 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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