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<P><FONT SIZE=2>Dear Gromacs users,<BR>
<BR>
I'm new to molecular dynamics and I face some problems with the analysis of my<BR>
trajectories.<BR>
<BR>
I intend to use the trjconv utility to extract frames from my trajectories. Each<BR>
trajectory can contain several frames that belong to different clusters. To do<BR>
this I create an .ndx file with the following structure<BR>
<BR>
[ output_file_name_1 ]<BR>
index1 index2 ... indexN<BR>
[ output_file_name_2 ]<BR>
index1 index2 ... indexM<BR>
<BR>
Then I pass this to trjconv in the following fashion:<BR>
<BR>
trjconv -s my_topology.gro -f my_trajectory.xtc -sub my_index_file.ndx<BR>
<BR>
I expect trjconv to split the trajectory into several xtcs, where the section<BR>
names in the index file are taken as the file names for the output. And each<BR>
newly created xtc will only contain these frames of the original trajectory that<BR>
where given as indices in the respective section of the .ndx file.<BR>
So is my understanding of the trjconv functionality correct so far???<BR>
<BR>
It tured out that this works most of the time, but fails sometimes. Sometimes<BR>
the last frame that was specified in the indices (indexN or indexM) is not<BR>
written. This also goes wrong (sometimes) when there is just a single index in<BR>
a section.<BR>
<BR>
What puzzeles me even more is that I get the error:<BR>
<BR>
｜ Double entries in block structure. Item 3 is in blocks 0 and 0.<BR>
｜ Cannot make unambiguous inverse block.<BR>
<BR>
for an innocuous looking index file with the content:<BR>
[ test ]<BR>
2 6 4 0<BR>
<BR>
Maybe there is something wrong with the 0. Doesn't the frame count start from 0?<BR>
Ah, and my gromacs version is 4.5.5.<BR>
<BR>
TIA,<BR>
Fabian Paul<BR>
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