Re: [gmx-users] trjconv - two chains are separated

Hi there, I had similar problems in the past. You'll have to play with trjconv and find the best combination of different flags to solve the visualization problem. You can start by trying out this workflow for example: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Re: [gmx-users] trjconv - two chains are separated

I have also encountered this problem and was able to solve it using the tpr file generated before running editconf as the input to trjconv (with -pbc no jump). Peter Sent from my iPad > On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos > wrote: > >

[gmx-users] trjconv - two chains are separated

Hi Gromacs Users, I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories. My protein has two chains (A and B) and they closely bind to each other. after running trjconv with "-pbc nojump", two chains are greatly separated by a certain distance. It is mostly likely that the

Re: [gmx-users] trjconv - two chains are separated

For "-pbc nojump" to work, you need to make sure they are together (as you want) in the first frame of your input trajectory. The most reliable way to do this is by centering the trajectory on a residue at the interface between the two chains (using a custom index group). I've also heard some