Hi Dallas, Thanks for your reply. I did try -pbc cluster for waters. It could fix it somehow but not completely. After that, I had to use -pbc center to fix it. Still, I do not get what I want. Unfortunately, some waters and lipids are appearing from the other side of the box.
Cheers, Mohsen On Sun, May 21, 2017 at 8:12 PM, Dallas Warren <dallas.war...@monash.edu> wrote: > 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 > dallas.war...@monash.edu > --------------------------------- > 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 > <ramezanpour.moh...@gmail.com> 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 gmx-users-requ...@gromacs.org. > -- > 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 gmx-users-requ...@gromacs.org. > -- *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 gmx-users-requ...@gromacs.org.