A collection of scripts and input files that might be useful to persons wishing to run molecular dynamics simulatons. These utilities are made to work well with downloads from GLYCAM-Web, but they should be usable in other situations, possibly with minor adjustments.
Used by GLYCAM-Web
These are the scripts used by GLYCAM-Web in its molecular modeling services.
We are very grateful to our funders.
Please check them out!
We use directories to organize things.
scripts : Contains executable scripts to do things such as start simulations.
inputs : Contains sets of inputs for different types of simulations.
In general, information in scripts will be related to information in inputs. For example, if a script refers to a set of mdin (molecular dynamics input file, AMBER style) files, those files will be somewhere in the inputs directory. The scripts will also be somewhat general, too, being customizable with just a few internal changes and able to use different sets of inputs.
For example, if you want to run a simulation that:
- Starts from a pre-minimized structure containing water.
- Relaxes the water first,
- Then relaxes everything,
- Then does a production run.
You would copy the file scripts/Run_Multi-Part_Simulation.bash and the three mdin files in inputs/pre-minimized-separate-water-relaxation/ into a directory with your pre-minimized parm7 and rst7 files. Then, you edit the Run_Multi-Part_Simulation.bash file as needed for your situation and then run the file.
You might also find scripts/Plot_MDEN.bash useful.