Hi Christoph, thank you, I figured it out. It required edits in the grompp energygrps in the gromacs.mdp.
On Monday, August 23, 2021 at 11:26:46 AM UTC-4 Christoph Junghans wrote: > 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. 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