Thank you. On Thursday, March 29, 2018 at 1:31:52 PM UTC-4, Christoph Junghans wrote: > > On Thu, Mar 29, 2018 at 10:25 AM, Alexander Alexander > <[email protected] <javascript:>> 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? >
Yes I will. > > > > > 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). > > If I simply copy the content of exclusions.txt to my topol.top file, then everything will be fine an no mismatching shows up between the rdf's (if rest is fine)? > > > > 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. > > Is the angle1.dist.tgt or bond.dist.tgt are the ones that "csg_boltsman *hist *..." gives us for a single molecule in vacuum? Any further refinement is needed to be performed on what hist gives us? In the hexane ibi_all example, there is a table.xvg file in the parent folder, I was wondering if we have to provide it in advance ourselves or the the votca would calculate it in the first step_000? Thank you. Best regards, Alex > > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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. 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