On Thu, Mar 29, 2018 at 10:25 AM, Alexander Alexander <[email protected]> wrote: > > Thanks. > I would be so thankful if one could comment on below questions; > > 1. The manual states that the IBI so far only supports iterative refinement > of non-bonded interactions, however, I saw an example of setting.xml file in > mailing list in which the bonded interactions were also defined for > refinement by IBI, so, does IBI also support the bonded interactions? Yes, it is supported for a while now! It seems we forgot to update the manual, where in the manual is it wrong? And can you send a pull request against https://github.com/votca/csg-manual to fix it?
> > 2. I guess the ensemble chosen for MD simulation during IBI depends on the > physics of the system (similar to the normal MD simulation), however, the > Tcoupl = 0 and Pcoupl = 0 has been assigned for the temperature and pressure > for all of the example of CG I have seen, so, I was wondering if the > ensemble should be similar to the all atoms MD simulation by which > target_rdf.xvg has been calculated, am I right? Yes, we usually do both simulations in NVT ensemble and we achieve that with a stochastic dynamics (sd) integrator in Gromacs. > > 3. We have to add the [ defaults ] and [ atomtypes ] section to the > topol.top generated by csg_gmxtopol, if I am not wrong the [ defaults ] > depends on the type of force field we want to use which should be again > similar to the target all atom MD simulation, for the [ atomtypes ], how I > should indicate the C6 and C12 parameter for each bead? of course the C6 and > C12 are available in ffnonbonded.itp for individual atoms involved in each > beads but not for the beads itself. For instance to get the mass of bead we > sum up the mass of individual atoms involved in that bead. When VOTCA creates the xvg tables for Gromacs, it writes the potential and forces in the C12 column, so you should set C12 to 1.0 (except if you need to scale it for some reason) and C6 to 0.0 (or whatever). > > 4. Below is a part of setting.xml file used in a IBI simulation; > > <name>ABA</name> > <min>1.2</min> > <max>2.9</max> > <step>0.001</step> > <inverse> > <!-- target distribution --> > <target>angle1.dist.tgt</target> > <do_potential>0 0 0</do_potential> > <post_update>smooth</post_update> > <post_update_options> > <scale>0.001</scale> > </post_update_options> > <post_add>convergence</post_add> > <gromacs> > <table>table_a1.xvg</table> > </gromacs> > </inverse> > </bonded> > <bonded> > Can you please confirm me that the <target>angle1.dist.tgt</target> is the > one we provide in advance and the <table>table_a1.xvg</table> is the one > which votca results after refinement? (in general for refinement of bonded > and nonbonded interaction <target>case.tgt</target> is the one we provide > and <table>case.table.xvg</table> is the votca give finally) > Also, how I can calculate the "angle1.dist.tgt" one? yes, <target> is the distribution VOTCA compares the current distribution against and <table> is the table VOTCA will generate from the update of that comparison, the filename is listed, so that you can setup your topology to use exactly the table with the same number. > > How should we know the <min>xx</min> and <max>xxx</max> for each > interaction? Just look at the distributions and pick min and max so that the distribution is bigger than 0 and that the extrapolation of the potentials will work (which is a bit of an art in itself). Christoph > > Thank you very much in advance for your time. > > Best regards, > Alex > > On Wednesday, March 28, 2018 at 3:28:44 AM UTC-4, Christoph Junghans wrote: >> >> On Tue, Mar 27, 2018 at 6:28 PM, Alexander Alexander >> <[email protected]> wrote: >> > >> > Thank Christoph. >> > Actually the xmlwf did not give more information than the parse error in >> > the >> > last line. >> > >> > I will take the opportunity to ask one more general question: >> > >> > Using the boltzmann inversion and iterative boltzmann inversion I wand >> > to >> > obtain the coarse-grained parameters (bonded and nonbonded) for a >> > molecule, >> > the molecule has 53 atom which I have mapped them on 5 beads (3 types) >> > and 4 >> > bonds and 3 angles. The all atom MD simulation for a system containing >> > 307 >> > molecules of my interest using gromacs and gromos force filed has also >> > been >> > completed. >> > As a new user, I found the votca manual too scattered (sorry for saying >> > that) to follow in order to obtain the CG parameters, I tried to >> > understand >> > the examples but still I am not able to fulfill the procedure. >> > >> > By considering the explained molecule I would be so appreciated if one >> > could >> > kindly itemize the steps I have to take to obtain all of the CG >> > parameters >> > of the molecule of my interest. >> There is no general practice, you will need to check the literature >> and find a system close to what you want to coarse-grain. >> You could trying to coarse-grain all interactions at once, but usually >> something will not work and make the system explode. >> I prefer to start small and build it up, so a.) Boltzmann invert the >> bonded interactions from a single molecule (in vacuum) trajectory, >> then b.) the non-bonded interactions with iterative Boltzmann >> inversion and last you might want to c.) re-iterate the bonded >> interactions. >> >> This has already been extensively discuss on this mailing list, so >> have a look in the archive. The hexane tutorial might be worth looking >> at, too. >> >> Christoph >> > >> > Thank you very much. >> > >> > Best regards, >> > Alex >> > >> > >> > >> > >> > On Tuesday, March 27, 2018 at 4:55:51 PM UTC-4, Christoph Junghans >> > wrote: >> >> >> >> On Tue, Mar 27, 2018 at 2:07 PM, Alexander Alexander >> >> <[email protected]> wrote: >> >> > >> >> > Solved now, I was missing a backslash in </ident>. >> >> > Anyway, thank you. >> >> The expat package, provides a little tool called "xmlwf", which allows >> >> you to check whether an xml file is well-formatted. >> >> >> >> Christoph >> >> > >> >> > Regards, >> >> > Alex >> >> > >> >> > >> >> > >> >> > On Tuesday, March 27, 2018 at 2:20:10 PM UTC-4, Alexander Alexander >> >> > wrote: >> >> >> >> >> >> >> >> >> Dear all, >> >> >> >> >> >> The "csg_dump --top case.tpr --cg case.xml" parses error at the last >> >> >> line >> >> >> of my case.xml with the mismatched tag, I can not find out where I >> >> >> am >> >> >> doing >> >> >> wrong, so, I would be so appreciated if you could have a look at my >> >> >> attached >> >> >> case.xml,.top,gro files and help me overcome the issue. >> >> >> >> >> >> Thanks >> >> >> Best regards, >> >> >> Alex >> >> > >> >> > -- >> >> > 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 post to this group, send email to [email protected]. >> >> > Visit this group at https://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > 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 post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
