On Wed, May 2, 2018 at 3:37 PM, Alexander Alexander <alexanderwie...@gmail.com> wrote: > Hi Christoph, > Thanks. > > On Wednesday, May 2, 2018 at 5:13:13 PM UTC-4, Christoph Junghans wrote: >> >> On Wed, May 2, 2018 at 1:38 PM, Alexander Alexander >> <alexand...@gmail.com> wrote: >> > Dear all, >> > I did a >> > My IBI-bonded-nonbonded (after getting the nonbonded potentials via >> > IBI-nonbonded only) crashes dues to the "...bonded interactions could >> > not be >> > calculated because some atoms >> > involved moved further apart ...". By replacing the ill-bond by a >> > harmonic >> > potential in topol.top file "2 3 N 0.3453 K" where N = 1,2 and K = >> > 5000, >> > the simulation are going well. Now what? what is the relation between >> > this >> > harmonic and the table_b2.xvg which was replaced by the harmonic one? >> > What >> > would happen for the table_b2.xvg? >> Sorry, I don't understand your question! Can you rephrase? >> > Let's say the calculation crashes when table_b2.xvg is used but it works > fine with "2 3 2 0.3453 1000" instead, then my question is that "should > I continue the preregistration using "2 3 2 0.3453 1000" and forget > about the table_b2.xvg? If so, what would be the final right table_b2.xvg at > the end? If not so, how I can take benefit from the knowledge of "2 3 2 > 0.3453 1000" to improve the table_b2.xvg so that it would work as well? You know generate a table with k*(r-r_0) (with r_0=0.3453 andk=1000, clip out the middle part and replace it with the structured part from BI.
> >> >> > Figures in attachment are the plot of >> > table_b2.xvg. >> > I got the bonded tables including the table_b2.xvg by "csg_boltzmann" >> > --> >> > "csg_call --sloppy-tables" ---> "csg_call --ia-type bond --ia-name bond >> > ... >> > gromacs table_b2.xvg". And I am using the bond(angle)-*.pot.in as >> > initial >> > guesses for my IBI-all. >> > >> > The table_b1.xvg in gromacs manual has been defined such that the the >> > r(nm), >> > f(r), f'(r) are the first, second and third column of table_b2.xvg where >> > f(r) is a cubic spline function in V_b(r_ij) = k*f(r_ij), If the same >> > definition is applied for the table_b2.xvg obtained by the above method? >> To be clear, the gromacs table format is x, f(x), -f'(x) (see gromacs >> manual 4.2.14) >> >> I am not sure what your question is! Gromacs uses cubic spline >> internal to interpolate the table. >> However, if you set cg.inverse.gromacs.table_bins in your xml file >> small enough (you had something like 0.002), then there isn't much to >> interpolate. >> >> >> > What is the unit of f(r)? >> KJ/mol (gromacs energy units) >> >> > What is the unit of each column in table_b2.xvg in VOTCA? >> KJ/mol/nm (gromacs force units) > > Just to sum up the table format, can you please confirm me that the > table_b.xvg in VOTCA has the following format: > first column : Distance with unit nm > Second column : Energy with unit KJ/mol > Thirst column: Force with unit KJ/mol/nm For bonds (not angles) in gromacs that is the format! Also for a different simulation backend, e.g. lammps this will be different of course, too! Christoph >> >> >> > >> > And would you please explain table_b2-1-3.png figure? >> Not sure what there is to explain..the code on how the third column is >> calculated is here: >> >> https://github.com/votca/csg/blob/master/share/scripts/inverse/table_to_xvg.pl#L95 > > Best regards, > Alex >> >> >> Christoph >> >> > Thank you very much. >> > Regards, >> > Alex >> > >> > -- >> > 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. 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.
