Hello,
I encountered a very strange (looks like legacy) issue with v1.4.1.
In my earlier IBI iterations (with v1.3) I normally used special
topol-rdf.tpr which was different from normal CG simulation topol.tpr by
not including the intra-molecular pairs in the RDF stats (done by
csg_stat). I wanted to make sure my previous results are reproduced by
v1.4.1, so copied all the initialisation files into a new directory and
tried to run once again. After the very first iteration I checked the
obtained RDFs and they were all wrong - corresponding to normal topol.tpr
(including intra-pairs) and not topol-rdf.tpr (excluding intra-pairs)!
I guess there might have been changes made to locations or names of tags in
settings.xml between the VOTCA versions, but I could not identify those
changes by referring to the most recent manual (both v1.4.1 and development
versions).
Below is the relevant extract from my settings.xml file.
Any clue, hint, advice are most welcome!
Thanks in advance.
Andrey
-----------
<gromacs>
<grompp>
<bin>gmx grompp</bin>
<!--opts></opts-->
</grompp>
<mdrun>
<!--command>grmx-vtc-rerun.sh</command-->
<!--command>mpirun -lsf mdrun_mpi</command-->
<!--opts>-multidir sim_0 sim_1 sim_2 sim_3</opts-->
<command>mpirun -n 4 mdrun_mpi</command>
<opts>-multidir sim_0 sim_1 sim_2 sim_3 -tablep table.xvg -tableb
table_b?.xvg table_a?.xvg table_d?.xvg</opts>
</mdrun>
<!--mdrun><opts>-nt 2</opts></mdrun-->
<!-- trash so many frames at the beginning -->
<equi_time>0</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.001</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>10000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.5</table_end>
<initial_configuration>maindir</initial_configuration>
<rdf>
<block_length><DESC>Length of the block for the error
analysis</DESC>
1000000
</block_length>
<map><DESC>Special mapping file for rdf calculations needed for
bonded interactions</DESC>
dopc_cg-map11.xml
</map>
<topol><DESC> Gromacs binary topol (tpr) file to be used for
csg_stat</DESC>
topol-rdf.tpr
</topol>
<with_errors>yes<DESC>calculate error on the rdf: yes/no</DESC>
</with_errors>
</rdf>
</gromacs>
-----------
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