Hello, Simple question. I am running MD simulations with GROMACS and getting the .xtc and .tpr output files in order to create a pdb video using trjconv. I am running simulations on a cluster, and so a pbs script must be submitted with the necessary commands. When using trjconv command, the group must subsequently be specified. Is there any way to modify the below command to also select a specific group (i.e. - 1 for 'Protein'). For example, when using mdrun, the -ff option can be used to specify which forcefield to use. Is there something similar to this with regards to the group selection when using trjconv? Thanks.
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
You could use
echo X | gmx trjconv ....
where X is the group of interest
If you want the separate pdbs use option -sep
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running