Thanks. On Monday, 5 June 2017 11:39:23 UTC-4, Christoph Junghans wrote: > > 2017-06-05 7:20 GMT-06:00 M. Chakraborty <[email protected] <javascript:>>: > > > 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 <[email protected]>: > >> > 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 [email protected]. > >> > To post to this group, send email to [email protected]. > >> > 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 [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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