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<div class="gmail_quote">On Thu, Jan 20, 2011 at 7:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="im"><br><br>bharat gupta wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">I loaded the .gro file generated after pdb2gmx command in vmd and then I loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD and when I click the play button on the toolbar the frames doesn't move ... can anybody tell me how to play the simula tion in VMD ?? or where am i going wrong<br>
<br><br></blockquote><br></div>How many frames did you save in the .trr file? Use gmxcheck. If it has multiple frames, it will load them all and you can watch the movie. Sounds like you haven't saved enough frames.<br>
<br>-Justin<br><br>
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<div class="im">-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>
South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>Mobile no. - 010-5818-3680<br></div>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>><br>
<br></blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<div><br><br clear="all">After running the simulation I checked the trajectory in using ngmx in some other system .. and it was working .. since I need to do some more analysis during trajectory run on my protein I thought of running into VMD and I used the file .trr after completng the simulation .</div>
<div> </div>
<div><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343</div>
<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>