I have found the cluster option of -pbc to work well for putting aggregates back together correctly. Some times you do need an index file and appropriate groups to assist with it getting it right.
gmx trjconv -pbc cluster Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 [email protected] --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On 16 May 2017 at 07:50, Mohsen Ramezanpour <[email protected]> wrote: > Dear Gromacs users, > > I have an HII phase made of one inverted cylinder (and waters inside) in a > triclinic box with 90, 90, 60 angles. After running the simulation, this > cylinder become bent like a curve. I.e. is not a perfect cylinder anymore. > As a result, some water molecules and lipids pass the box sides and enter > from the other side of box because of PBC. > Now, I want to make the cylinder again but I am not sure how to do so. > > The best I could do was to use "-pbc mol -ur compact" options in trjconv. > However, here are still some lipids and molecules which are not part of the > cylinder. > > Any idea how could I fix the effect of these PBC in visualization? > > Thanks > Mohsen > > -- > *Rewards work better than punishment ...* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
