W dniu poniedziałek, 1 lipca 2013 15:31:48 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/1 <[email protected] <javascript:>>: > > > > > > 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> >
Thanks a lot! > > > > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
