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?
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, <[email protected] <javascript:>> > 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] <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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