Got it! Thanks! On Tuesday, November 17, 2015 at 11:28:58 AM UTC-6, Christoph Junghans wrote: > > Hi, > > > 2015-11-16 21:00 GMT-07:00 MSW <[email protected] <javascript:>>: > > > > 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 [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/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de >
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