[gmx-users] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?

Dear all, I have two question: 1) Are the atom types I chose for the use of OPLS force field correct? I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg Server converts PDB files of drug structures just in an .itp file

Re: [gmx-users] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?

Meyer-Almes, Franz-Josef, Prof. Dr. wrote: Dear all, I have two question: 1) Are the atom types I chose for the use of OPLS force field correct? I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg Server

[gmx-users] Visualization Problem

Hi, I finished a simulation of a carbon nanotube in water. I made a movie of the simulation using 'trjconv' to view with Pymol. The problem is that starting from the third frame it messes the carbon nanotube bonds. I changed the start time and again in the third frames it messed things

Re: [gmx-users] Visualization Problem

Shalom George Maybe your nanotube 'jump' over the PBC? Try 'trjconv -pbc whole ...' Best, Itamar George Abadir wrote: Hi, I finished a simulation of a carbon nanotube in water. I made a movie of the simulation using 'trjconv' to view with Pymol. The problem is that starting from the

Re: [gmx-users] Visualization Problem

Thanks Itamar for your reply, but the tube actually does not jump, but the lines showing the bonds start to show bonding between non-neighbouring atoms, i.e., the hexagonal shape characteristic of nanotubes is destroyed, and it starts from the third frame regardless of the start time. I tried

RE: [gmx-users] Visualization Problem

Probably means that atoms are moving across the pbc boundary from one side of the box to another. The visualiser you are using is trying to maintain the bond between the atoms after the move, so draws it all the way across the box itself. Two ways to fix, don't visualise the bonds, using either