Hello VOTCA folks,
Since LAMMPS dump files provide no topological information, I'm doing as
instructed in the manual and using a XML topology. However, I'm not quite
sure how to specify more than one bond of a single type.
To simplify my question, suppose I have a bead-spring polymer model with 8
beads per chain (this would be the reference system). My topology XML file
looks like this in this case:
<topology name="traj.dump">
<molecules>
<clear/>
<molecule name="CHAIN" nmols="1000" nbeads="8">
<bead name="A1" type="1" mass="1.0." q="0.0"/>
<bead name="A2" type="1" mass="1.0." q="0.0"/>
<bead name="A3" type="1" mass="1.0." q="0.0"/>
<bead name="A4" type="1" mass="1.0." q="0.0"/>
<bead name="A5" type="1" mass="1.0." q="0.0"/>
<bead name="A6" type="1" mass="1.0." q="0.0"/>
<bead name="A7" type="1" mass="1.0." q="0.0"/>
<bead name="A8" type="1" mass="1.0." q="0.0"/>
</molecule>
</molecules>
<bonded>
<bond><name>bond</name><beads>CHAIN:A1 CHAIN:A2</beads></bond>
<bond><name>bond</name><beads>CHAIN:A2 CHAIN:A3</beads></bond>
<bond><name>bond</name><beads>CHAIN:A3 CHAIN:A4</beads></bond>
<bond><name>bond</name><beads>CHAIN:A4 CHAIN:A5</beads></bond>
<bond><name>bond</name><beads>CHAIN:A5 CHAIN:A6</beads></bond>
<bond><name>bond</name><beads>CHAIN:A6 CHAIN:A7</beads></bond>
<bond><name>bond</name><beads>CHAIN:A7 CHAIN:A8</beads></bond>
</bonded>
</topology>
There is a single bond type in the system, i.e., the bonds A1-A2, A2-A3,
..., A7-A8, are all of the same type. I've tried to list them in a single
<bond> block, however it didn't allow me to do that. What seems to work is
the setup shown above, where multiple <bond> blocks all have the same name.
My intention is to tell that all these bonds are of the same type. Does
this setup work as intended? As I said, it seems to work, but I don't know
whether I'm doing it in the proper way of if it's only working by accident.
My VOTCA version is 1.4_rc1.
Cheers,
Gustavo
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