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hello David<br>
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<pre wrap=""><span class="moz-txt-citetags"></span>
<span class="moz-txt-citetags">> </span>is there a unit problem when comparing trajectory and tpr files ?
<span class="moz-txt-citetags">> </span>can it be that N is called atom 1 in the trajectory file and atom 0 in
<span class="moz-txt-citetags">> </span>the topol.tpr file?
<span class="moz-txt-citetags">> </span>
<span class="moz-txt-citetags">> </span>if gmxcheck is working correctly, then my topol.tpr is completely
<span class="moz-txt-citetags">> </span>wrong, how can I find out the mistake?
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From gmxcheck -h :
If both a trajectory and a tpr file are given (with -s1) the program will
check whether the bond lengths defined in the tpr file are indeed correct in
the trajectory. If not you may have non-matching files due to e.g.
deshuffling or due to problems with virtual sites. With these flags,
gmxcheck
provides a quick check for such problems.
So are you sure the tpr file and the trajectory match?
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thanks for your answer. <br>
well, I am not working in parallel and I don't have virtual sites, so I
was already excluding non-matching problems related to these cases.
What else could it be and how do I check if files are matching or not? <br>
I tried with gmxdump -s topol.tpr and indeed the first atom in
topol.tpr is a N and has number 0, but I thought this is always the
case.<br>
btw I have just tried gmxcheck -f traj.trr -s1 topol.tpr on the
tutorial files... also there I get this long list ... what am I doing
wrong?<br>
<br>
thanks again<br>
<br>
Grazia<br>
<br>
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