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? 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? What is the unit of f(r)? What is the unit of each column in table_b2.xvg in VOTCA? And would you please explain table_b2-1-3.png figure? 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.
