Thanks Christoph Junghans for connecting me to Christoph Scherer. Hello Christoph Scherer, I am have 3 particle coarse grain mapping of methanol in the form AOH where A represents the methyl group. CG simulation with force-matched potentials is exploding and gives energies to be nan. I am trying do diagnose the problem and want to extract the forces or between O and H in the original trajectory. I have uploaded the settings xml file and the mapping file. I interested in extracting only the non-bonded potentials and have a trajectory recalculated with exclusion groups (as described in the paper: Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane). I even tried modifying the settings file to have only the non-bonded interactions between O and H. I still get nan for forces when I ran force matching with the modified settings xml file.
Thank you! Regards, M. Chakraborty On Friday, 28 July 2017 12:31:50 UTC-4, Christoph Scherer wrote: > > Hi, > > you can run csg_fmatch with the --no-map option. Then it will act on the > original Gromacs trajectory with the Gromacs Atom names. The question is > what exactly do you mean by pairwise force? csg_fmatch will give you the > average force between the specific atom pairs averaged over all! > interactions if you choose nonbonded pair interactions in the --options > file. > > Best Christoph > > -- 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.
methanol.xml
Description: XML document
setting.xml
Description: XML document
