<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><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 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></div><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? <br><br>Thanks for your help.<br><br></pre><div> </div><div>Sincerely,<br>Shima<br></div> <div style="font-family: arial, helvetica,
sans-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> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <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> </font> </div> <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 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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<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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