Hi,
2015-11-16 21:00 GMT-07:00 MSW <mohd.alwaraw...@gmail.com>: > > Dear VOTCA users, > > I am trying to calculate the other bonded distributions that I did not > iterate over during each iteration. I am iterating over the angle term only > but I want to see how the bond and dihedral terms change. I just want to > calculate the bond and dihedral distribution without iterating or producing > potential for them. There are two way of doing what you want: 1.) list all interaction in your settings file, but set do_potential=0 for those you don't want to iterate. or 2.) Overload "rdf gromacs" by a script which uses a different settings.xml file (see section 91. of the manual for details) > > I used the following example, but I still produce potential for bond and > dihedral. I think because I included "<inverse> </inverse>" > > <cg> > <bonded> > <!-- bond --> > <name>bond1</name> > <min>0.236000</min> > <max>0.292000</max> > <step>0.001</step> > <inverse> > <target>bond1.dist.tgt</target> > <gromacs> > <table>table_b1.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <!-- angle --> > <name>angle1</name> > <min>1.100175</min> > <max>1.801287</max> > <step>0.001</step> > <inverse> > <target>angle1.dist.tgt</target> > <do_potential>1</do_potential> > <post_update>scale</post_update> > <post_update_options> > <scale>0.010000</scale> > </post_update_options> > <post_add>convergence</post_add> > <gromacs> > <table>table_a1.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > <!-- dihedral --> > <name>dihedral1</name> > <min>-1.510723</min> > <max>2.801333</max> > <step>0.01</step> > <inverse> > <target>dihedral1.dist.tgt</target> > <gromacs> > <table>table_d1.xvg</table> > </gromacs> > </inverse> > </bonded> > <inverse> > <kBT>2.49435</kBT> > <program>gromacs</program> > <gromacs> > <equi_time>200</equi_time> > <table_bins>0.002</table_bins> > <pot_max>1000000</pot_max> > <table_end>5.0</table_end> > <topol>topol.tpr</topol> > <traj>traj.xtc</traj> > <mdrun> > <opts> -nt 4 </opts> > </mdrun> > </gromacs> > <map>NCP_CG.xml</map> > <filelist>grompp.mdp topol.top table.xvg index.ndx table_b1.xvg > table_d1.xvg </filelist> > <iterations_max>1</iterations_max> > <convergence_check> > <type>default</type> > <limit>5</limit> > </convergence_check> > <method>ibi</method> > <log_file>inverse.log</log_file> > <restart_file>restart_points.log</restart_file> > </inverse> > </cg> > > Thanks > > Mohammad > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
