Dear Users,
My system consists of a molecule (butane) made of 4 beads with 2 types A
and B. I want to extract bonded parameters. I use csg_stat:
csg_stat --top nvt.tpr --cg cg.xml --options settings.xml --trj nvt.xtc
where cg.xml
<cg_molecule>
<name>BUT</name>
<ident>Other</ident>
<topology>
<cg_beads>
<cg_bead>
<name>b1</name>
<type>CH3</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:BUT:C1 1:BUT:H1 1:BUT:H2 1:BUT:H3 </beads>
</cg_bead>
<cg_bead>
<name>b2</name>
<type>CH2</type>
<symmetry>1</symmetry>
<mapping>B</mapping>
<beads> 1:BUT:C2 1:BUT:H4 1:BUT:H5 </beads>
</cg_bead>
<cg_bead>
<name>b3</name>
<type>CH2</type>
<symmetry>1</symmetry>
<mapping>B</mapping>
<beads> 1:BUT:C3 1:BUT:H6 1:BUT:H7 </beads>
</cg_bead>
<cg_bead>
<name>b4</name>
<type>CH3</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:BUT:C4 1:BUT:H8 1:BUT:H9 1:BUT:H10 </beads>
</cg_bead>
</cg_beads>
<cg_bonded>
<bond>
<name>bond</name>
<beads>
b1 b2
b2 b3
b3 b4
</beads>
</bond>
<angle>
<name>angle</name>
<beads>
b1 b2 b3
b2 b3 b4
</beads>
</angle>
<dihedral>
<name>dihedral</name>
<beads>
b1 b2 b3 b4
</beads>
</dihedral>
</cg_bonded>
</topology>
<maps>
<map>
<name>A</name>
<weights> 12 1 1 1 </weights>
</map>
<map>
<name>B</name>
<weights> 12 1 1 </weights>
</map>
</maps>
</cg_molecule>
settings.xml
<cg>
<fmatch>
<constrainedLS>0</constrainedLS>
<frames_per_block>6</frames_per_block>
</fmatch>
<bonded>
<name>bond</name>
<fmatch>
<min>0.155</min>
<max>0.175</max>
<step>0.005</step>
<out_step>0.0002</out_step>
</fmatch>
</bonded>
<bonded>
<name>angle</name>
<fmatch>
<min>1.5</min>
<max>2.2</max>
<step>0.05</step>
<out_step>0.0002</out_step>
</fmatch>
</bonded>
<bonded>
<name>dihedral</name>
<fmatch>
<min>0.1</min>
<max>5.5</max>
<step>0.05</step>
<out_step>0.0002</out_step>
</fmatch>
</bonded>
</cg>
I got the error: property not found: step
But it is defined, so what is the problem?
Steven
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