[gmx-users] Molecule Jumps

[Mark Abraham]

darrellk at ece.ubc.ca wrote:
> Hi All,
> I have an array of molecules above a grapehene sheet in my simulation.
> However, when I look at my trajectory file (.trr) in VMD the array of
> molecules is split into 4 sections with each section located at what
> looks to be the corners of the simulation box. And the graphene sheet
> does not stay stationary as it should, but rather jumps from corner to
> corner. I tried to resolve this problem by running the following command:
> 
> trjconv -f traj.trr -o trajout.trr -center -pbc nojump
> 
> However, this did not resolve the problem. Is there something else I need
> to do to resolve this problem?

No, some combination of options to trjconv should work. Sometimes two 
two separate invocations with separate options are needed.

BTW "...does not stay stationary as it should" is not true... you're 
wanting a certain feature for your visualization convenience, and during 
the simulation GROMACS hadn't permitted you to choose which of the 
infinite equivalent possibilities it should present in the trajectory. 
You're choosing that now, *after* the fact.

Mark