2017-06-02 13:16 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > This might me be more of a gromacs problem but still I am posting it here. I > ran a CG simulation of methanol where I have used two bead representation > for each methanol molecule. I have used force-matching to generate tabulated > potential. I have used almost the same grompp.mdp file as found in the > methanol tutorial (I only added the groups and added constraints to the > bonds). Even though I had set pbc as xyz, when I viewed my trajectory I saw > many of the particles going outside the box. I am not sure why pbc is not > working. I have added my cg_grompp.mdp and cg topology file. You can use "gmx trjconv -pbc mol" to make a trajectory with molecules whole concerning to pbc or "gmx trjconv -pbc atom" to make trajectory with atoms whole concerning to pbc.
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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
