Dear Christoph, Thank you for your informative response.
>From what I learned reading the manual and mailing list, below I summarize the step needed to parameterize the CG FF (both bonded and nonbonded) for a molecule using *IBI*, I am sure it save a lot of time for new users, I hope you could correct me wherever needed; What we have initially is *single-mol-vacuum-aa.gro* file. 1. Creating the desired *mapping.xml* from the *single-mol-vacuum-aa.gro .* 2. Generating the exclusions list using over the single molecule: csg_boltzmann --top *single-mol-vacuum-aa.tpr* --cg mapping.xml --excl *exclusions.txt.* 3. Adding the *exclusions.txt* to the *single-mol-vacuum-aa.top *and conduction an atomistic MD simulation for the single molecule in vacuum to have a new *single-mol-vacuum-aa-excl.tpr *and *single-mol-vacuum-aa.trr* . 4. Defining a *setting-bonded.xml* for the bonded interactions. 5. Calculating the bonded parameter using the "csg_stat --top *single-mol-vacuum-aa-excl.tpr* --trj *single-mol-vacuum-aa.trr* --cg *mapping.xml* --nt 4 --options *setting-bonded.xml* --begin 20000. Now we have all bonded interaction (*bonded.dist.new* renamed to* bonded.dist.tgt*) which can be taken later in IBI. 6. Generating a bigger system from the single molecule, *bigger.gro* and conducting an atomistic MD smilulation for the bigger system (again we have to use the *exclusions.txt *list here !? ). 7. Crreating a neww setting file in which only the nonbonded interactions have been defined, * setting-nonbonded.xml.*8. Now we can calculate the RDF either using gmx rdf in gromacs or csg_stat in votca over the bigger system "csg_stat --top *bigger.tpr* --trj *bigger.trr* --cg *mapping.xml* --nt 4 --options *setting**-nonbonded.xml* --begin 2000. The RDF is needed only for those pairs which we are interested in their nononbonded interaction. Now, we also have the *nonbonded.dist.new* renamed to *nonbonded.dist.tgt* files. 9. Combining the both *settting-bonded.xml *and *setting-nonbonded.xml *to a *setting.xml *and adding the parameters needed for *IBI *of both bonded and nonbonded to it. 10. Mapping the bigger atomistic system to a CG system to have* bigger-CG.gro *using "csg_map --top *bigger.tpr* --trj *bigger.trr* --cg *mapping.xml* --out *CG.gro*. 11. Having the *bigger-CG.gro,* *setting.xml, **bonded.dist.tgt and **nonbonded.dist.tgt *along with other files needed for a normal MD simulation using gromacs (coulombtype and vdw-type = User), we can start iteration (csg_inverse --options settings.xml) to have finally our table_bonded.xvg and table_nonbonded.xvg files. On Friday, March 30, 2018 at 4:51:53 AM UTC-4, Christoph Junghans wrote: > > On Thu, Mar 29, 2018 at 12:14 PM, Alexander Alexander > <[email protected] <javascript:>> wrote: > > 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]> 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? > > > The lines which need updating are in page 31 of manual section 7.2.1. I do not have github account to pull a request over there. Best regards, Alex > > > > 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)? > The exclusions are for the atomistic vacuum run, but yes, the theory > is that the exclusions will help. > > >> > >> > > >> > 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? > Yes, csg_boltzmann or csg_stat, which can also calculate bonded > distributions as well. > Refinement is only needed, if you have some invalid point in between > min and max, otherwise you should be good. > For IBI of bonded interactions, you should use the same normalization > as csg_stat does, i.e. calculated the distributions with csg_stat, > e.g. with: > $ csg_stat --trj atomistic.xtc --top atomistic.tpr --cg mapping.xml > --options interactions.xml > > > > > 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? > The table.xvg was needed for older versions of gromacs and if I recall > correctly not needed anymore with gromacs-2016. > In a nutshell, gromacs needed a catch-all table for all the > interactions not covered by special interactions e.g. table_CG_CG.xvg, > even if the rest group was empty. > If all interactions are covered by special interactions, which is > usually the case, then table.xvg could be a table full of zeros. > > Christoph > > > > 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]. > >> > 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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