On Sat, Aug 17, 2019 at 3:08 AM Souvik Chakraborty <[email protected]> wrote: > > Thanks, Christoph. > > Before csg_inverse, the force is still very high even after several em steps > on conf_cg.gro. But, my atomistic trajectory was well-equilibrated. > > I am not not sure how to get the force within tolerance for a CG geometry. > Should I equilibrate the atomistic trajectory more, and start from scratch? This really depends on the system, but I would have a look at the table in step_001 and see if they look ok to start with. Usually the initial condition, which is what you get from mapping the atomistic trajectory, isn't super important, but it might be worth minimizing it with just repulsive lennard-jones.
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/4c072f72-e174-4fc1-8e36-fe4ce9b65092%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/CAHG27e6rn-BygJ0LJ7s0AHrJWA7xOKnOq78M%3Dsz8%2BbrbdvoOKA%40mail.gmail.com.
