After I added the pressure correction, the density of the cg system is very close to the full-atomic system. Thanks for your advise. But when I use these final potential table to do the tensile simulation for cg system, the system is unstable. And the stress-strain curve is extrmely terrible. I saw someone abtained a good stress-strain curve at https://groups.google.com/forum/#!msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ . So I want to know how could I get a good stress-strain curve with these potential table? Or there still need some post process for these table?
在 2018年12月3日星期一 UTC+8下午10:58:40，Christoph Junghans写道： > > On Mon, Dec 3, 2018 at 3:51 AM Lee <[email protected] <javascript:>> > wrote: > > > > Yes, you are right. I missed a important item, pressure > correction. But when I add pressure into the <post_update>, the error > occurred "Pressure correction for lammps is not implemented yet". Does the > pressure correction need to be implemented additionally? And how to > implement it? > > Well it just means we haven't added support for pressure correction > when using lammps in that version. > However, it has been added here https://github.com/votca/csg/pull/201, > so either patch that in or use the development version of votca > instead (see > https://github.com/votca/votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions.) > > > > Christoph > > > Thanks > > > > 在 2018年12月3日星期一 UTC+8上午10:48:57，Christoph Junghans写道： > >> > >> On Sun, Dec 2, 2018 at 6:40 PM Lee <[email protected]> wrote: > >> > > >> > By checking the convergence value of interaction, I found that it was > stabilized above 1. When I use these potential table to do the cg > simulation, the density of cg system is half of that the corresponding > atomic system. So I think the nonbond interaction is still immature. How to > reach a lower convergence number? The rdf and the convergence number of C-C > are attched. > >> > >> Run longer iterations, finer binsize, in general everything which > >> increases the statistics helps. > >> > >> On the other hand, your RDF conversion looks pretty good already, > >> don't let this one number guide you, you need to test the > >> coarse-grained model, too. > >> > >> Christoph > >> > > >> > 在 2018年12月1日星期六 UTC+8下午9:44:34，Christoph Junghans写道： > >> >> > >> >> On Fri, Nov 30, 2018 at 8:00 PM Lee <[email protected]> wrote: > >> >> > > >> >> > OK, thanks! I have increased the bin size and the > distribution seems to be smoothed. > >> >> > In some paper, the IBI process is started from bond and then > angle, the nonbonded potential is finished at last. When doing ibi for bond > and angle, the pair interaction is turned off. The chains are pushed apart > to remove close contacts by slowly turning on a soft, purely repulsive > potential as you said before. But I couldn't find the command in lammps. > >> >> That might be a question for the lammps mailing list! > >> >> > >> >> > Another question, how could I output the value of > convergence for every iterative step? > >> >> The convergence numbers are stores in a files for each interaction > >> >> called <NAME>.conv and the sum is printed in the log files, so you > can > >> >> do: > >> >> $ grep "Convergence sum" inverse.log > >> >> > >> >> This of course assumes you enabled the convergence check feature > (with > >> >> setting cg.inverse.convergence_check.type to "default") > >> >> > >> >> Christoph > >> >> > > >> >> > 在 2018年11月30日星期五 UTC+8下午11:24:33，Christoph Junghans写道： > >> >> >> > >> >> >> > >> >> >> > >> >> >> On Fri, Nov 30, 2018 at 01:05 Lee <[email protected]> wrote: > >> >> >>> > >> >> >>> In votca, the smoothing process works for potential. Is there > any smoothing process for new distribution? And what's the command? > >> >> >> > >> >> >> No, but it would be hard to add! > >> >> >> > >> >> >> Also increasing the bin size naturally does smoothing! > >> >> >> > >> >> >> Christoph > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> 在 2018年11月21日星期三 UTC+8下午9:03:19，Christoph Junghans写道： > >> >> >>>> > >> >> >>>> On Tue, Nov 20, 2018 at 6:44 PM Lee <[email protected]> > wrote: > >> >> >>>> > > >> >> >>>> > The expression of boltzmann inversion is V=-kBTln(P). And the > distribution P is related to the scale of the x-coordinate. The plot of > bond distribution with different units are attached. In votca, all the > processes including calculating distributions and boltzmann inversion are > finished with units nm. So can I say that the obtained potential table used > in lammps is converted by V=-kBTln(P) with the length units nm? So in > lammps, the dynamic simulation is finished with length units angstroms but > with the potential corresponding to units nm. > >> >> >>>> > >> >> >>>> Well, V(x)= -kBTln(P(x)) and x can be a distance or an angle > etc. V > >> >> >>>> and P are always parameterized by the same variable in its > units. Also > >> >> >>>> P(x) is a distribution and hence is unit-less, plus the > normalization > >> >> >>>> of the distribution doesn't matter much as ln(a*P)=ln a + ln P > and > >> >> >>>> hence only leads to an irrelevant offset in the potential and > doesn't > >> >> >>>> matter to the forces. > >> >> >>>> > >> >> >>>> Christoph > >> >> >>>> > >> >> >>>> > > >> >> >>>> > 在 2018年11月20日星期二 UTC+8下午11:43:59，Christoph Junghans写道： > >> >> >>>> >> > >> >> >>>> >> On Tue, Nov 20, 2018 at 2:04 AM Lee <[email protected]> > wrote: > >> >> >>>> >> > > >> >> >>>> >> > I have another question. If my units command is real > in lammps which the units of distance and energy are angstroms and > Kcal/mole respectively, what shoud I change in the setting file in order to > get the potential table with right units? Now, the bond and angle potential > of the CG system are much lower than the corresponding atomic system. > >> >> >>>> >> > >> >> >>>> >> Usually VOTCA calculated things in Gromacs units (so nm, > kJ/mol etc.), > >> >> >>>> >> but if you only calculate RDFs you don't need to change > anything as > >> >> >>>> >> input and output are both in nm and hence there is no > scaling > >> >> >>>> >> involved. So this will work for angstroms as well. > Additionally, you > >> >> >>>> >> need to make sure that kBT is in the right unit in the > settings file. > >> >> >>>> >> > >> >> >>>> >> Christoph > >> >> >>>> >> > Thanks a lot. > >> >> >>>> >> > > >> >> >>>> >> > 在 2018年11月20日星期二 UTC+8上午5:52:29，Christoph Junghans写道： > >> >> >>>> >> >> > >> >> >>>> >> >> On Mon, Nov 19, 2018 at 8:51 AM Christoph Junghans < > [email protected]> wrote: > >> >> >>>> >> >> > > >> >> >>>> >> >> > On Sun, Nov 18, 2018 at 8:31 PM Lee < > [email protected]> wrote: > >> >> >>>> >> >> > > > >> >> >>>> >> >> > > For the dynamic simulations finished with lammps, > should I set the exclusions? If excluding non-bonded interactions between > atoms that are no further than 3 bonds away, does it need to excluding > these atoms when statistical target rdf distributon? > >> >> >>>> >> >> > > > >> >> >>>> >> >> > Yes, for LAMMPS you will most likely need to create rdf > exclusion manually. > >> >> >>>> >> >> > > >> >> >>>> >> >> > You can check, what exclusion VOTCA see by running: > >> >> >>>> >> >> > $ csg_dump --top <your_topology_file> --excl > >> >> >>>> >> >> > > >> >> >>>> >> >> > For advanced topology handling see, section 3.3 of the > manual, > >> >> >>>> >> >> > http://doc.votca.org/manual.pdf > >> >> >>>> >> >> Also Joshua might be able to say something about the new > LAMMPS > >> >> >>>> >> >> topology reader in csg and how exclusions are > incorporated there. > >> >> >>>> >> >> > >> >> >>>> >> >> Christoph > >> >> >>>> >> >> > > >> >> >>>> >> >> > Christoph > >> >> >>>> >> >> > > -- > >> >> >>>> >> >> > > 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 > >> >> >>>> >> >> > >> >> >>>> >> >> > >> >> >>>> >> >> > >> >> >>>> >> >> -- > >> >> >>>> >> >> 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. > >> >> >> > >> >> >> -- > >> >> >> 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] <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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