2014-12-01 18:11 GMT-07:00 Vitalie Botan <[email protected]>: > Hi there, > > I have a Lammps trajectory and corresponding topology and mapping XML files, > so everything seems to work fine with csg_boltzmann and csg_stat scripts and > I am able to generate CG-tables both for bonded and non-bonded interactions. > However, when I try to convert resampled and extrapolated bonded potential > with the following script csg_call convert_potential lammps > got this message: > > ERROR: > > potential_to_generic.sh: conversion of bonded interaction to generic tables > is not implemented yet! Most of the code is already there, it is just not enabled, because I have never used tabulated bonded interaction in LAMMPS. Do you have a specification for LAMMPS' bonded tables? (i.e. what's in the 1st, 2nd, 3rd column for bond, angle and dihedral tables?)
> > > Is there any proper way to prepare a smoothed extrapolated bonded potential > for Lammps? You could use csg_call convert_potential gromacs instead, gromacs' bonded tables are just three columns. (r, U(r), F(r)) I've tried csg_resample with --derivative option together with > the smoothed potential from csg_boltzmann output, but all the table values > were marked with "o" sign, meaning they will be extrapolated later, and > exactly this scenario one has to avoid when preparing tabulated potential > for Lammps. You could change it by hand from "o" to "i", or run the csg_call potential extrapolate [OPTIONS] input output Christoph > > --Vitalie > > > PS: I am using 1.3-dev version of votca. > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
