Options "-mdp" and "-dir" do not work together in martinate

marrink-lab / gromit

Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using gromacs

GNU General Public License v2.0

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Options "-mdp" and "-dir" do not work together in martinate #24

Closed jmelcr closed 4 years ago

jmelcr commented 4 years ago

Options "-mdp" and "-dir" do not work together in martinate. It seems that the mdp file is expected to be in the simulation directory, but the path to it (from the argument of -mdp) is static and/or the mdp file is not copied to the new folder. An example code invoking this problem is: martinate.sh --insane-l=DPPC:168 --insane-sol=W --insane-d=10.0 --insane-dz=25 --insane-pbc=rectangular -dir sim01 -mdp my_mdp_file.mdp

Tsjerk commented 4 years ago

I see that currently -dir will have more conflicts. Is the feature desirable, of is it better to remove it and leave setting up a new subdirectory to a user or enveloping script?