2015-10-12 10:34 GMT-06:00 Christoph Junghans <[email protected]>: > 2015-10-12 7:04 GMT-06:00 frank Zack <[email protected]>: >> Hi Christoph, >> thank you for your help. Its really a brilliant tool even though its quite >> hard to handle.But I've already put so much time in trying to make it >> work...so I dont want to give up. >> My "test-project" is very similar to the hexane-ibi-bonded example. I only >> did minor modifications to the xml-files. >> >> The mapping file: >> >> <cg_molecule> >> <name>HEX</name> >> <ident>hexane</ident> >> <topology> >> <cg_beads> >> <cg_bead> >> <name>SC1</name> >> <type>SC1</type> >> <mapping>UNITY</mapping> >> <beads>1:hex:SC1</beads> >> </cg_bead> > Something is wrong here, your molecule has only one CG bead! > To calculate angle distribution you need at least 3 beads, e.g. SC1, > SC2, SC3 all of type SC. Adding to that look at hexane_cg.xml in hexane/ibi_bonded it also has 3 beads and you could all 3 of the same type to make it homogeneous mapping.
> > Christoph > >> </cg_beads> >> <cg_bonded> >> <bond> >> <name>bond</name> >> <beads> >> SC1 SC1 >> </beads> >> </bond> >> <angle> >> <name>angle</name> >> <beads> >> SC1 SC1 SC1 >> </beads> >> </angle> >> </cg_bonded> >> </topology> >> <maps> >> <map> >> <name>UNITY</name> >> <weights>1</weights> >> </map> >> </maps> >> </cg_molecule> >> >> the settings-file: >> <cg> >> <bonded> >> <name>bond</name> >> <min>0.1</min> >> <max>0.45</max> >> <step>0.0002</step> >> <inverse> >> <!-- target distribution --> >> <target>bond.dist.tgt</target> >> <gromacs> >> <table>table_b1.xvg</table> >> </gromacs> >> </inverse> >> </bonded> >> <bonded> >> <!-- name of the interaction --> >> <name>angle</name> >> <min>0.0</min> >> <max>3.0</max> >> <step>0.0001</step> >> <inverse> >> <!-- target distribution --> >> <target>angle.dist.tgt</target> >> <gromacs> >> <table>table_a1.xvg</table> >> </gromacs> >> </inverse> >> </bonded> >> <!-- example for a non-bonded interaction entry --> >> <non-bonded> >> <!-- name of the interaction --> >> <name>A-A</name> >> <!-- types involved in this interaction --> >> <type1>SC1</type1> >> <type2>SC1</type2> >> <!-- dimension + grid spacing of tables for calculations --> >> <min>0</min> >> <max>1.5</max> >> <step>0.01</step> >> <inverse> >> <!-- target distribution (rdf), just give gromas rdf.xvg --> >> <target>A-A.dist.tgt</target> >> <!-- update cycles --> >> <do_potential>1 0 0</do_potential> >> <!-- additional post processing of dU before added to potential --> >> <post_update></post_update> >> <!-- additional post processing of U after dU added to potential --> >> <post_add>convergence</post_add> >> <!-- name of the table for gromacs run --> >> <gromacs> >> <table>table_SC1_SC1.xvg</table> >> </gromacs> >> </inverse> >> </non-bonded> >> <!-- general options for inverse script --> >> <inverse> >> <!-- 300*0.00831451 gromacs units --> >> <kBT>2.49435</kBT> >> <!-- use gromacs as simulation program --> >> <program>gromacs</program> >> <!-- gromacs specific options --> >> <gromacs> >> <!-- trash so many frames at the beginning --> >> <equi_time>150</equi_time> >> <!-- grid for table*.xvg !--> >> <table_bins>0.002</table_bins> >> <!-- cut the potential at this value (gromacs bug) --> >> <pot_max>1000000</pot_max> >> <!-- extend the tables to this value --> >> <table_end>2.5</table_end> >> </gromacs> >> <map>hexane_cg.xml</map> >> <!-- these files are copied for each new run --> >> <filelist>grompp.mdp topol.top table.xvg index.ndx</filelist> >> <!-- do so many iterations --> >> <iterations_max>500</iterations_max> >> <convergence_check> >> <type>default</type> >> <limit>0.001</limit> >> </convergence_check> >> <!-- ibm: inverse biltzmann imc: inverse monte carlo --> >> <method>ibi</method> >> <!-- write log to this file --> >> <log_file>inverse.log</log_file> >> <!-- write restart step to this file --> >> <restart_file>restart_points.log</restart_file> >> </inverse> >> </cg> >> >> Trajectory-file (~100MB): >> https://www.dropbox.com/s/lmzir99zkth5srt/traj.xtc?dl=0 >> >> (p.s. tut mir echt leid,dass nerven muss...Es lässt mich einfach nicht los, >> ich will unbedingt coarse grainen ^^) >> >> -- >> 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/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- 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/d/optout.
