2017-06-05 7:20 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Thanks for your reply. However, my problem is not broken atoms/molecules. I > expect to see broken molecules at the boundary when pbc is set. But for my > simulation, the molecules are intact but they are moving beyond the box > even though pbc is set. Sorry, I should have explained myself a bit better. With "gmx trjconv -pbc atom" you should be able to fold all coordinates back into the 1st image of the simulation box. However, I am not sure why you would want that, any thermodynamics for the trajectory will need to be calculated using minimum image convention anyhow, so having some atom sticking out won't hurt.
Christoph > > On Friday, 2 June 2017 18:23:05 UTC-4, Christoph Junghans wrote: >> >> 2017-06-02 13:16 GMT-06:00 M. Chakraborty <maghe...@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+un...@googlegroups.com. >> > To post to this group, send email to vo...@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. -- 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.
