[gmx-users] trjconv -pbc

Carla Jamous carlajamous at gmail.com
Thu Sep 16 13:42:51 CEST 2010

Hi everyone,

please I'm doing a simulation of a dimer with a ligand.

When I want to visualize my trajectory, I have the problem that my dimer or
my ligand or both diffuse out of the box and I don't have a continuous

I tried many options:

1)trjconv -center -pbc mol -ur compact (centering on protein)

2) trjconv -center -pbc mol (centering on the ligand)

3) trjconv -center -pbc atom (centering on ligand)
    and then, trjconv -pbc whole

4) trjconv -pbc nojump
    and then trjconv -fit rot+trans

5) trjconv -center -pbc mol (centering on protein)
    and then trjconv -fit rot+trans

6) trjconv -center -pbc mol -ur compact (centering on ligand)
    and then -fit rot+trans

*all of these options didn't work*

I tried a last one:

trjconv -center -pbc atom -ur compact (centering on ligand)
and then trjconv -pbc nojump
and then trjconv -fit rot+trans

this one is the best one but I still have one part of my molecule that
diffuses out of the box at one point in my trajectory.

Please I'm out of ideas, can anyone give me a hint on how to get a fully
continuous trajectory entirely centered in my box?

Thank you

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