Dear Gustav,
W dniu czwartek, 27 października 2016 15:16:58 UTC+2 użytkownik Gustavo
Rondina napisał:
>
> 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.
>
>
There should be no issue with creating a bond definition that contains
multiple beads, like here:
<bonded>
<bond>
<name>bond</name>
<beads>
CHAIN:A1 CHAIN:A2
CHAIN:A2 CHAIN:A3
CHAIN:A3 CHAIN:A4
CHAIN:A4 CHAIN:A5
CHAIN:A5 CHAIN:A6
CHAIN:A6 CHAIN:A7
CHAIN:A7 CHAIN:A8
</beads>
</bond>
</bonded>
Did you get some error if you have xml topology defined in that way? Could
you provide us the error message?
Also you can check how VOTCA is interpreting topology by using csg_dump:
csg_dump --top topol.xml
and you can look into the exclusion lists retrieved from the topology by:
csg_dump --top topol.xml --excl
If bonded section is read correctly then you should see it in the exclusion
lists.
Best regards,
Jakub
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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