2013/7/1 <[email protected]>: > > > W dniu poniedziałek, 1 lipca 2013 15:09:12 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/7/1 <[email protected]>: >> > I am trying to run IBI for angles. I calculated 88 distributions for >> > angles >> > (its a protein made of 90 beads) using csg_boltzmann. >> > >> > My question: shall I refine and smooth those ditributions? >> > >> > In my xml: >> > >> > <bonded> >> > <name>angle</name> >> > <min>1</min> >> > <max>3</max> >> > <step>0.05</step> >> > <inverse> >> > <target>angle.dist1</target> >> > <gromacs> >> > <table>table_a1.xvg</table> >> > </gromacs> >> > </inverse> >> > </bonded> >> > >> > How can I add the remaining angles so votca will know which angle >> > corresponds to which x y z atoms? >> > >> > Would that be >> > >> > <bonded> >> > <name>angle</name> >> > <min>1</min> >> > <max>3</max> >> > <step>0.05</step> >> > <inverse> >> > <target>angle.dist1</target> >> > <gromacs> >> > <table>table_a1.xvg</table> >> > </gromacs> >> > </inverse> >> > </bonded> >> > <bonded> >> > <name>angle</name> >> > <min>1</min> >> > <max>3</max> >> > <step>0.05</step> >> > <inverse> >> > <target>angle.dist2</target> >> > <gromacs> >> > <table>table_a2.xvg</table> >> > </gromacs> >> > </inverse> >> > </bonded> >> > etc? >> > >> > Or am I missing somethin and I should provide with one distribution >> > corresponding to all angles? Please, advise. >> You will have use different names for the different angles, something >> like angle1, ..., angle9 or angle_A_B_C ,..., angle_X_Y_Z. >> Remember that the names in the settings xml file and the mapping file >> have to be the same. >> >> Christoph > > > Thank you. So in settings file for angle names: angle1, angle2 etc the > mapping should be: > > <cg_bonded> > > <angle> > <name>angle1</name> > <beads> > 1MET 2SER 3VAL > </beads> > > <angle> > <name>angle2</name> > <beads> > 1GLY 2SER 3ARG > </beads> > > Am I correct? Looks ok. > > How csg_inverse know the name of the mapping file? It is not specified in > the input of csg_inverse. The mapping file is given in the settings xml file (see the hexane/ibi_bonded tutorial): <cg><inverse><map>mappping.xml</map></inverse></cg>
> > Steven > >> > >> > 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. >> > 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. > 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. For more options, visit https://groups.google.com/groups/opt_out.
