Thanks Christoph for the clarification. I have one more point to understand. I have read in some paper that, the IBI process is started from bond and then angle, then the nonbonded potential is finished at last. When doing ibi for bond and angle, the pair interaction is turned off. How is this turning off done.
While trying to do sequentially, If I want to do IBI of a bond type, say A-B first. Do I still be needing tabulated potentials for angle or non-bonded types using csg_inverse. I generated a table_b0.xvg file for A-B bond using commands csg_boltzman and csg_call and put it in main directory and then I run csg_inverse. But my simulation stops at step_001 asking for other table_b1.xvg (other bond) and table_a1.xvg (other angle) files. The error is: "Tabulated interaction of type 'Tab. Angles' with index 0 cannot be used because no table file whose name matched '_a0.xvg' was passed via the gmx mdrun -tableb command-line option" Also while taking all interactions at once in settings.xml, simulation stops at step_001 stating: "Fatal error: A tabulated bond interaction table number 1 is out of the table range: r 2.030714, between table indices 1015 and 1016, table length 1001" I want to know, how I can optimize bond, angle, dihedral and then non-bonded potentials one by one and run IBI simulation. I am attaching the settings.xml file that I used for getting A-B potential only using csg_inverse and the table_b0.xvg file for AB bonded interaction. Thanks, Pragati On Monday, 20 July 2020 18:00:26 UTC+5:30, Pragati Sharma wrote: > > Dear all, > > I am simulating a polymer using IBI. I have a confusion, at what step is > the coarse grained trajectory is generated and used. > > > The process I am following is: > > 1.csg_mapp : To generate out.gro using mapp.xml > > 2. csg_stat : To generate distributions, but it also uses the atomistic > trajectory traj_comp.xtc > csg_stat --top topol.tpr --trj *traj_comp.xtc* --cg mapp_5mer.xml > --options settings.xml > > > 3. csg_boltzmann : To generate potentials, but it also uses the atomistic > trajectory traj_comp.xtc > csg_boltzmann --top topol.tpr --trj *traj_comp.xtc* --cg mapp_5mer.xml < > boltzmann_cmds > > 4. csg_call: To smoothen the potentials > > 5. csg_inverse: > > csg_inverse --options settings.xml > *Excerpts from Settings.xml:* > > <map>buta_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>50</iterations_max> > > I think in this 5th step only, a CG trajectory is generated and used. > Am I correct with the steps. > Also, are the distributions generated from csg_stat are the target ones > that are to be compared with the ones obtained from last step of > csg_inverse. > > Thanks > Pragati > > > -- 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/5d57a405-dbf3-4728-b4de-43977e5b84a4o%40googlegroups.com.
settings.xml
Description: XML document
table_b0.xvg
Description: Binary data
AB.bond.dist.new
Description: Binary data
AB.bond.pot.ib
Description: Binary data
