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.
