On Mon, Aug 20, 2018 at 1:40 AM <jjbm.resea...@gmail.com> wrote: > > Hello, again. > > I think I have the same problem in such early steps. I didn't pay attention > because I thought that this medium range structure would disappear over > further iterations, and was focusing on the fact that the convergence > tendency was blown up at certain point. But now it occurs to me that the > cause of all these issues (sinusoidal structure and inability to converge) > may be due to the exclusion lists been different when computing the target > RDF and the ones used by default by VOTCA. Because the manual is quite > oriented to GROMACS with the topology of the AA representation (as opposed to > the CG topology when using LAMMPS), maybe I am doing some assumption that > should not be done. The excluded pair interactions when determining the > target RDFs are 1-2, 1-3 and 1-4 interactions (for all bead combination, as > it is a very simple molecule). Therefore, the origin of the problem could be > VOTCA not excluding some of those bead pairs when determining the new RDFs. > What are the default values for exclusion lists? Could it be the problem? How > do I generate them when using LAMMPS?
You can use "csg_dump --top topol.xml --excl" to check the exclusions if they are wrong, you can either add: - phantom bonds in your topol.xml to add more exclusions. - use the data file as topology instead (only available in votca-1.5) Christoph > > Javier > > El jueves, 16 de agosto de 2018, 13:28:16 (UTC+1), Christoph Junghans > escribió: >> >> Ok, I ran this simulation for a couple of iterations, but in my case >> you can already see a structure developing in the A-A rdf after >> step_001, which get worse after every iteration, I only did 7 steps. >> With structure I mean the rdf has like a sinus wave on it, usually >> that is a sign that the molecules aren't moving enough. And the same >> thing is also obvious from watching the traj.dump file using VMD. >> >> I am not sure why it happened so quickly for me already, but I am >> using LAMMPS 16 Mar 2018 and VOTCA 1.5-dev gitid: 12f8b60. >> So it might be worth trying to use the development version of VOTCA. >> >> Christoph >> >> On Wed, Aug 15, 2018 at 2:02 AM, <jjbm.r...@gmail.com> wrote: >> > Sorry I forgot the data file. I attach it now. >> > >> > Javier >> > >> > El martes, 14 de agosto de 2018, 19:22:49 (UTC+1), Christoph Junghans >> > escribió: >> >> >> >> On Tue, Aug 14, 2018 at 8:03 AM, <jjbm.r...@gmail.com> 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, <jjbm.r...@gmail.com> 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 votca+un...@googlegroups.com. >> >> >> > To post to this group, send email to vo...@googlegroups.com. >> >> >> > 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 votca+un...@googlegroups.com. >> >> > To post to this group, send email to vo...@googlegroups.com. >> >> > 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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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