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, <[email protected]> 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, <[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. -- 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.
