In GROMACS how do I know how many box images a particular atom has moved from from t=0 to t=N? LAMMPS, for example, has the option to include image flags in the dump file for x, y, and z. Is there any way I can automatically know which simulation box image a particular atom is in a GROMACS .gro or similar file? The command I used to generate instantaneous coordinates is the following:
gmx trjconv -s trajectory.tpr -f trajectory.xtc -o coord.gro -pbc whole
Where trajectory.tpr and trajectory.xtc are outputs of a completed NPT simulation.
Dear Iskinder Arsano,
I really don't know if there is a easier way, but my siggestion is to use the "-pbc nojump" option of gmx trjconv. According to the manual: "this ensures a continuous trajectory but molecules may diffuse out of the box". You can then check all x, y and z coordinates of the desired atom in the desired frame and calculate how many box lengths it diffused along the simulation.
Hope it helps.
Best,
Felippe
Thank you very much Felippe Colombari - I tested -pbc nojump and it does provide the unwrapped coords. This will do.
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