On Wed, May 2, 2018 at 1:38 PM, Alexander Alexander <[email protected]> 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?
> 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) > > 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 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 [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.
