On Thu, Aug 15, 2019 at 6:36 AM Souvik Chakraborty <[email protected]> wrote: > > > Update: I could figure out how to include flags to 'gmx mdrun' in > settings.xml. The error is still the same. I probably need to energy-minimize > the conf.gro well before csg_inverse.
One can do an energy minimization before every step if needed, we call it a pre-simulation, see here: https://github.com/votca/csg-tutorials/blob/master/spce/simplex/simple/settings.xml#L57-L59 You just need to specify an additional mdp file (and/or topology file if needed). Christoph > > Regards, > Souvik > > On Wednesday, 14 August 2019 20:40:19 UTC+8, Souvik Chakraborty 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? Is there any way to customize the 'gmx mdrun' >> command inside the scripts? >> >> >> 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) >> >> >> 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/a4d05a4f-e028-473e-b0d5-e86edef176b8%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/CAHG27e6bd_1r7CjYp5Rp6o4TeuqY0W0o5Rz9YOq%2B5YtwSzU%3DPw%40mail.gmail.com.
