On Sat, Aug 21, 2021 at 10:13 PM Satyen Dhamankar <[email protected]> wrote: > > 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. I would look at the mapping file agian, it seems after the 1:1 mapping there is a "WT" in the topology (see the unknown molecule warning above) , but in your settings.xml you are referring to TW, so my guess you either want to change the water to "TW" in water.xml or "WT" in the settings.xml.
Top debug this you can run: csg_dump --top topol.tpr --cg "1nipam.xml;water.xml" and check what votca reads. Christoph > > > -- > 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. -- Christoph Junghans Web: http://www.compphys.de -- 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/CAHG27e4ubPXf0q9J9Ly%2BF2F0dxZ_FQWeUHvR2zqYPzJdRNtSgA%40mail.gmail.com.
