I need to perform some MD calculations and then trajectories of some small molecules analyzed.
What I have is
- cofactor (FAD)
- small molecule (either single O2 molecule or single Chlorine atom)
- crystallographic waters
The software I can access is Gromacs (with yum install)
I have tried and tried to get this to run (for 6 months perhaps), to no avail. The input files located on the web do not work on the version of Gromacs provided by the yum install command.
Is there a kind soul somewhere that would have suitable input files that would do all the steps described below and who'd be willing to pass them on to me?
What needs to be done is:
- add waters to the crystallographic waters in order to fill a box of suitable size
- generate parameter and topology files for each component separately
- merge these into global parameter and topology files for the system
- run initial Energy Minimization
- run M.D. simulations
- analyze the trajectories of the small molecules.