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.
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 -- 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.
