Hello, I am running a coarse-grained simulation of a 3-bead molecule (2 bonds+1 angle) in a coarse-grained, single-bead, solvent (water) bath. I have successfully run the gromacs all-atom trajectories, and I am using votca to run the IBI simulation.
>From the all atom simulation, I obtained the solvent-solvent rdf, the 2 bond distributions, and the single angle distributions using csg_stat and csg_boltzmann. Then, I am running: csg_inverse --options settings.xml where settings.xml is: <cg> <non-bonded> <name>TW-TW</name> <!-- types of molecules involved in this interaction --> <type1>TW</type1> <type2>TW</type2> <!-- dimensions + grid spacing of tables for calculations --> <min>0</min> <max>1.4</max> <step>0.01</step> <inverse> <!-- target distribution (rdf) --> <target>TW-TW.dist.tgt</target> <!-- update cycles --> <do_potential>1</do_potential> <!-- additional post processing of dU before added to potential --> <post_update>scale smooth</post_update> <post_update_options> <scale>1</scale> <!-- scale the potentials before updating it --> <smooth> <iterations>2</iterations> </smooth> </post_update_options> <post_add></post_add> <gromacs> <table>table_TW_TW.xvg</table> </gromacs> </inverse> </non-bonded> <bonded> <name>BO1</name> <min>0.217</min> <max>0.253</max> <step>0.001</step> <inverse> <target>BO1.dist.tgt</target> <gromacs> <table>table_BO1.xvg</table> </gromacs> </inverse> </bonded> <bonded> <name>BO2</name> <min>0.227</min> <max>0.288</max> <step>0.001</step> <inverse> <target>BO2.dist.tgt</target> <gromacs> <table>table_BO2.xvg</table> </gromacs> </inverse> </bonded> <bonded> <name>ANG1</name> <min>1.877</min> <max>2.998</max> <step>0.001</step> <inverse> <target>ANG1.dist.tgt</target> <gromacs> <table>table_ANG1.xvg</table> </gromacs> </inverse> </bonded> <!-- general options for inverse script --> <inverse> <kBT>2.7437884</kBT> <program>gromacs</program> <map>1nipam.xml</map> <map>water.xml</map> <gromacs> <equi_time>20</equi_time> <table_bins>0.001</table_bins> <pot_max>1000000</pot_max> <table_end>2.5</table_end> <mdrun> <opts>-nt 8</opts> </mdrun> </gromacs> <filelist>grompp.mdp topol.top table.xvg index.ndx table_a1.xvg table_b1.xvg</filelist> <!-- do so many iterations --> <iterations_max>5</iterations_max> <convergence_check> <type>default</type> <limit>0.001</limit> </convergence_check> <method>ibi</method> <log_file>inverse.log</log_file> <restart_file>restart_points.log</restart_file> </inverse> </cg> I am getting the following error: # critical: 'csg_stat --nt 28 --options settings.xml --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0 --cg "1nipam.xml;water.xml";' failed # After I go in step_001 and try the above command, I get: I get a wall of text saying: WARNING: unknown molecule "WT" with id XXXX in topology molecule will not be mapped to CG representation Check weather a mapping file for all molecule exists, was specified in --cg separated by ; and the ident tag in xml-file matches the molecule name. Topology does not have beads of type "TW" This was specified in type1 of interaction "TW-TW" I don't understand where this message is coming from. I have a 1nipam.xml file which has the information about the CG of my monomer molecule, and water.xml file which has the information about the CG scheme of my water molecule. I would appreciate any advice you have for me. -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/2ab517e0-762c-4083-865c-867ef9e1033dn%40googlegroups.com.
