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<div class="moz-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" href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank"><span class="" id="lw_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?
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<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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