<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><br></span></div><div> OK, but as I know the trjconv is a command after mdrun, so when I get the output of mdrun and see it in VMD, it doesn't make different. <br>Now wondering what is the benefit of trjconv -center and -pbc?<br><br></div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b>
Friday, June 15, 2012 8:24 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] protein near the edges of simulation box<br> </font> </div> <br>
<br><br>On 6/15/12 11:46 AM, Shima Arasteh wrote:<br>> Dear Elton,<br>> Where am I supposed to use trjconv -center ? when I want to get the mdrun?<br><br>trjconv is a post-processing command that can be used for a variety of purposes, of which one of the more common ones is to transform coordinates for convenient visualization through operations involving -center or -pbc.<br><br>-Justin<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]<a target="_blank" href="http://vt.edu/">vt.edu</a> | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br><br><br> </div> </div> </div></body></html>