On Tue, Aug 14, 2018 at 8:03 AM, <[email protected]> wrote: > Hi, Christoph, > > thanks for your quick answer. > >> What version of VOTCA are you using? (Run "csg_call --version") > > The version I am using is 1.4.1. It might be worth trying the development version: https://github.com/votca/votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions We have improved the lammps backend quite a bit.
> >>The "step_000/A-A.dist.tgt" in your plot, doesn't seem to be the same > as you send around. >>Why is the one in the plot, so rough? > > I think the plot I sent in my previous message does not show it very well. > The red curve is the target (which is not well visible under all the rest) > and the brown one is the divergent result. I attach a new graph showing only > target, convergent-looking curve at step 270, and divergent result at step > 360. The bin size for the RDFs is 0.1 Angstroms. Ok, the 270 result doesn't look too bad even though there is something funky going on around 12 AA. > >> Also, there are a bunch of files missing to test your system, so I > cannot check. nut I would certainly start with harmonic potentials for > the bonds. > > I started with harmonic potentials, but I changed to Boltzmann inverted ones > to check whether that was the problem. Can you send your data file as well? > >>And if you are doing IBI on the non-bonded interactions only, you > don't need a mapping file. > > I thought I needed it but, anyway, it was not affecting the coarse-graining, > right? True if you give the atoms the right type in the mapping file. I have seen case where the non-bonded interactions differed due to wrong (different) types. > >>Plus the pressure correction block should be somewhere inside an > interaction block, but again make it simple and start without pressure > correction. > > thanks, I take note of it. > > I attach the new figure with only three curves, including the target and > diverged curves, and also the potentials and distributions required to run > the simulations. > > I must insist that the problem I have also happened to me with no smoothing, > averaging and pressure correction options, and with harmonic potentials > instead of tables for the bonds and angles. I added these features > sequentially to check whether any of them was causing the problem. I will > redo the simplest example and post results and files here. In the meantime, > what could possibly be causing the divergence? In step 360 the RDF don't even approach 1 for larger distances, it might be that your system formed a crystal (or something), so it might be worth watching the MD movie of step 360 and look for something strange going on. Christoph > > Kind regards. > Javier > > El martes, 14 de agosto de 2018, 14:06:24 (UTC+1), Christoph Junghans > escribió: >> >> On Tue, Aug 14, 2018 at 3:04 AM, <[email protected]> wrote: >> > Hello, >> > >> > I am trying to obtain the coarse-grained non-bonded potentials for a >> > dodecane model of type ABBA with LAMMPS. I am no sure what I am doing >> > wrong >> > since the RDFs seem to tend to converge to the target functions, and >> > after >> > some steps they completely diverge. I tried smoothing the potentials, >> > and >> > other tricks (averaging , scaling, pressure corrections, etc) but I am >> > not >> > sure what I am doing wrong. >> > >> > I attach the RDFs functions for a number of steps, and the votca files I >> > am >> > using. I hope you can give me any hint to continue. >> What version of VOTCA are you using? (Run "csg_call --version") >> >> The "step_000/A-A.dist.tgt" in your plot, doesn't seem to be the same >> as you send around. >> Why is the one in the plot, so rough? >> >> Also, there are a bunch of files missing to test your system, so I >> cannot check. nut I would certainly start with harmonic potentials for >> the bonds. >> And if you are doing IBI on the non-bonded interactions only, you >> don't need a mapping file. >> Plus the pressure correction block should be somewhere inside an >> interaction block, but again make it simple and start without pressure >> correction. >> >> Christoph >> > >> > Kind regards and thank you in advance. >> > >> > -- >> > 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.
