2013/3/15 <[email protected]>: > 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? the fmatch block is too much, min,max and step have to be under bonded/non-bonded directly. csg_stat doesn't read the fmatch block. Force matching has its own min,max, step (defined in the fmatch block) as the requirement on the statistics are slightly stronger than for distributions.
I would recommend adding both blocks, so that you can do force matching and IBI with the same settings file. Christoph > > Steven > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
