<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Atila,<div>Coincidentally, the answer is almost the same as my previous posting a few minutes ago! <div><br></div><div>You can view Gromacs trajectories (.tpr tpology file and .trr portable binary trajectory file). I believe these formats have changed from time to time with different Gromacs versions, but if you get a recent version of Chimera (version 1.5) it should cover these possibilities.<div><br></div><div>Trajectories are shown with the MD Movie tool (start it by choosing Tools... MD/Ensemble Analysis... MD Movie from the Chimera menu). That gives a file browser for opening trajectory formats.<br><br>MD Movie documentation includes a list of the possible formats, and much more about the tool:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html</a>></div><div><br></div><div>Also, the following tutorial, part 1, uses MD Movie to view a sample Amber trajectory (data provided along with the tutorial):</div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html</a>></div><div><br></div><div>(Part 2 also uses MD Movie, but on different data, an NMR ensemble from the PDB.)</div><div><br></div><div>The documentation and tutorials are also included with your download and can be accessed from the Chimera Help menu. I hope this helps,</div><div>Elaine</div><div><div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><div><div>----------</div><div>Elaine C. Meng, Ph.D. </div><div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div><br></div></div></span></div><div><div>On Nov 1, 2010, at 3:26 AM, atila petrosian wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi chimera users</div>
<div>I did simulation of protein by gromacs. I want to see my trajectory during simulation by a viewr other than vmd, such as chimera. </div>
<div>How and what files is needed for that? <br>-- <br>Atila Petrosian<br>Ph.D. student of BioPhysical Chemistry<br>University of Oulu,Finland<br></div></blockquote></div><br></div></div></div></div></body></html>