Dear Sir,<br><br> I used dodecahedron for the simulation. My specific doubt was whether<br>do we need to modify the .xtc file using some options of -pbc like nojump, <br>mol, before going for analysis or we can directly go for analysis using the<br>
raw .xtc file.<br><br>Thanking you<br>With regards<br>M. Kavyashree<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br><br><div class="gmail_quote">
---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Mark Abraham</b> <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
Date: Fri, Jun 3, 2011 at 12:58 PM<br>Subject: Re: [gmx-users] option -pbc in trjconv<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im">
<br><br><br><div>
On 3/06/2011 3:42 PM, Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Dear users,<br>
<br>
I wanted to ensure that the option of -pbc in trjconv is only for visualization,<br>
and if I do all possible calculations with the original .xtc file there wont be any<br>
problem.<br>
</blockquote>
<br></div></div>
-pbc is for any purpose you can think of. Some analyses of periodic simulations only make sense for some representations of the unit cell. Some don't. Read about the tool, think carefully, then act :-)<br>
<br>
Mark<br><font color="#888888">
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</font></div><br><br clear="all"><br>-- <br>Yours Sincerely,<br>Dr. Shankar Prasad Kanaujia<br>Research Associate<br>C/O - Professor K. Sekar<br>Bioinformatics Centre<br>Indian Institute of Science, Bangalore-12<br>Phone: +919480258032<br>
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