On Mon, Jul 20, 2020 at 06:30 Pragati Sharma <[email protected]> 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. > Yes, that is both correct, csg_inverse will generate the CG trajectory in each step and compare its distributions to the target ones that you generated with cag_stat in step 2. Christoph > > 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/1d6edb99-6e4b-4ec6-802a-98a4cc545be3o%40googlegroups.com > <https://groups.google.com/d/msgid/votca/1d6edb99-6e4b-4ec6-802a-98a4cc545be3o%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAHG27e7V8Pheiuzn4v2kXL9geOHG2aM1i3cKa8JHM3%2B83MEY-A%40mail.gmail.com.
