Hi Christoph, Thank you again. On Saturday, March 31, 2018 at 5:02:49 AM UTC-4, Christoph Junghans wrote: > > On Fri, Mar 30, 2018 at 9:34 AM, Alexander Alexander > <[email protected] <javascript:>> 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. > > If the bonded parameters are also iterated, how much the computational cost increase usually? One more confirmation please concerning to the ensemble used in each simulation: single-mole-vacume should be in NVT, should sd integrator is used here? with md the final structure was normal whereas by sd integratorgave me a weird structre after 80 ns, something like the attached final gro file, although I used NPT, that might be the reason.
bigger system atomistic simulation should be in NVT? Again, md or sd integrator? If so, I have to redo some simulation which I have performed in NPT with md integrator. The iteration CG simulation of bonded and nonbonded should defiantly be performed in NVT with sd integrator. I used a <step>0.0001</step> in setting.xml, so that mmight be the reason of getting too noisy bonded.dist.new file specially for the angles, am I right please? Also, I see in the literature, like the original votca paper, that the angles have been plotted vs degree which is bettere, but what csg_stat gives me for angles is vs number not degree, I was wondering how I can convert that? For a system with 5 bead if it is really necessary to define dihedral? what if I do not consider? In noticed that the dihedral has not been that much paid attention in your examples. > > > > 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. > Ok , thanks. But the exclusions should be considered in the IBI iteration by adding it to the topol.top file used in IBI iteration, if I am not wrong.!? > > > > 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) > That is me, but I am not aithub guy and do not use it, so I am not familiar with it. But I will try again. Best regards, Alex > > 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] <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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prdsd.gro
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