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