On Fri, Mar 30, 2018 at 9:34 AM, Alexander Alexander <[email protected]> wrote: > > 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. You could also Boltzmann invert them right now and only iterate the non-bonded interactions to start with.
> > 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 !? ). Just do a normal full melt simulation (without exclusions) to get the RDFs of the non-bonded interactions. > > 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]> 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. Fixed here: https://github.com/votca/csg-manual/pull/7 and that seems to be you: https://github.com/AlexanderWi (or somebody is misusing your gmail address) Christoph > > 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]. >> > 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.
