On Wed, Aug 14, 2019 at 6:40 AM Souvik Chakraborty <[email protected]> wrote: > > Dear group members, > > While running csg_inverse to get non-bonded potential, I get the following > error in inverse.log: > > Fatal error: > 1 of the 4500 bonded interactions could not be calculated because some atoms > involved moved further apart than the multi-body cut-off distance (1.5 nm) or > the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and > tabulated bonds also see option -ddcheck > > > ###################################################################### > > How to solve this error? This usually means a bond got stretched too far, so something isn't setup correctly.
> Is there any way to customize the 'gmx mdrun' command inside the scripts? Yes. It is the cg.inverse.gromacs.mdrun.command option in the xml file. (see sec. 10.5.83 of http://doc.votca.org/manual.pdf) > > > Another issue: How to include exclusions in topol.top? > (I have created the file exclusions.txt, and included it in topol.top. But, > csg_inverse cannot find it) Did you forget to exclusions.txt add to the <filelist>? Christoph > > > Thanks in advance! > > -Souvik > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/ad305ca4-49c4-4017-9690-98f9bf8a8e6a%40googlegroups.com. -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7_F_fvm%2Bvvx%3DHmpY2gg%2BXDTpqFzBo7s8KThgzRYyY_EQ%40mail.gmail.com.
