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On 3/06/2011 6:48 PM, Kavyashree M wrote:
<blockquote
cite="mid:BANLkTikejT790S3KbrHWFnj7Aeb_kwWpkw@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Maybe. Only a general answer can be given to a general question.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikejT790S3KbrHWFnj7Aeb_kwWpkw@mail.gmail.com"
type="cite">Thanking you<br>
With regards<br>
M. Kavyashree<br>
<br>
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---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Mark Abraham</b> <span
dir="ltr"><<a moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a>>
<div class="im">
<br>
<br>
<br>
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On 3/06/2011 3:42 PM, Kavyashree M wrote:<br>
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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>
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</div>
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-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>
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Yours Sincerely,<br>
Dr. Shankar Prasad Kanaujia<br>
Research Associate<br>
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