Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Hi Justin Thanks for the suggestions. However, I don't really want to stop the molecule moving into the next image-I start off with an alkyl chain where a large portion of the structure overlaps the pbc. i.e C1-C2-C3 \\ C4-C5-C6 where || is the unit cell boundary. To see the whole alkyl c

Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Jennifer Williams wrote: Hi Justin Thanks for the suggestions. However, I don't really want to stop the molecule moving into the next image-I start off with an alkyl chain where a large portion of the structure overlaps the pbc. i.e C1-C2-C3 \\ C4-C5-C6 where || is the unit cell boundary

Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Dear Jenny, You can do this directly in VMD, using the Periodic tab under Graphics->Representations. Ran Jennifer Williams wrote: > > > Hello, > > I am trying to find a way around a visualisation problem I am having > in VMD. Some of my molecules go over periodic boundary conditions > meaning th

Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Jennifer Williams wrote: Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in

[gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in VMD but as yet no luck