[gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD?

[Juan Munoz-Garcia]

I'm a new GROMCAS user. I've run an NVT equilibration of a explicitly solvated protein-ligand complex, I've extracted frames throughout the trajectory in both .pdb and .gro format and I've open them in VMD and I've checked the simulation's gone fine . However, when I try to open in VMD either the .trr or .trj trajectory file just the water box appears (as white single-point dots, not the whole water molecule) but not the protein or ligand. Have any of you experienced this issue before? Could it be a problem of the .trr/.trj VMD plugins? I'd really appreciate you commentaries.

Thank you.
Regards.

Juan C. Munoz-Garcia, PhD
Biomembrane Structure Unit
University of Oxford	
South Parks Road
Oxford OX1 3QU
juan.munoz-garcia at bioch.ox.ac.uk