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<div class="moz-cite-prefix">On 19/06/2012 5:49 PM, Shima Arasteh
wrote:<br>
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cite="mid:1340092196.80446.YahooMailNeo@web36404.mail.mud.yahoo.com"
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<div><span>Thanks for your reply.</span></div>
<div><br>
<span></span></div>
<div><span>I entered the trjconv as the workflow of </span><a
moz-do-not-send="true" rel="nofollow" target="_blank"
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions"><span
class="yiv319367622" id="yiv319367622lw_1340080873_1">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</span></a><br>
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<pre class="yui_3_2_0_20_134007912458383" style="margin: 0em; font-family: arial,helvetica,sans-serif;">And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stframe.pdb ), which I produced earlier?
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We don't know what you've done. Try it and see... the whole purpose
is whether you like the form of what you see, right?<br>
<br>
Mark<br>
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cite="mid:1340092196.80446.YahooMailNeo@web36404.mail.mud.yahoo.com"
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<pre class="yui_3_2_0_20_134007912458383" style="margin:0em;font-family:arial, helvetica, sans-serif;">
Thanks for your help.
</pre>
<div> </div>
<div>Sincerely,<br>
Shima<br>
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<div style="font-family: times new roman, new york, times,
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<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Tuesday, June 19, 2012 11:00 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] Trjconv error<br>
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<div class="yiv319367622moz-cite-prefix">On 19/06/2012
4:13 PM, Shima Arasteh wrote:<br>
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<pre style="margin:0em;font-family:arial, helvetica, sans-serif;">Dear gmx users,
I want to follow the workflow regarding to
<a moz-do-not-send="true" rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions"><span class="yiv319367622" id="yiv319367622lw_1340080873_1">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</span></a>
for the second step I enter the command as below:
trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
But I get the error:
Index[232] 235 is larger than the number of atoms in the
trajectory file (234). There is a mismatch in the contents
of your -f, -s and/or -n files
I don't have any index file, so what this error is talking about?</pre>
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Then it must mean there's a mismatch in the contents of
your -f and -s files... each must refer to the same
system. Something about your past management of these
two files makes your intended operation a nonsense, but
we can't know what. If, for example, you chose xtcgroups
in your .mdp file as something other than System, then
they do not.<br>
<br>
Mark<br>
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style="color:#000;background-color:#fff;font-family:times
new roman, new york, times, serif;font-size:12pt;">
<pre style="margin:0em;font-family:arial, helvetica, sans-serif;"> How may I solve it? Anybody may suggest me any solution please?
</pre>
<div style="font-family:arial, helvetica,
sans-serif;"> I would be so thankful for your
suggestions.<br>
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<div style="font-family:arial, helvetica,
sans-serif;">Sincerely,<br>
Shima</div>
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