Simulations

This page should help you running simulations with Hippo.

To run a simulation you will need

• hippo executable and data files in a directory which we will denote by HIPPO_HOME
• a pdb file for your system
• a hippo_input.txt

The standard protocol is:

1. make a working directory
2. copy your input files (pdb and hippo_input.txt) into the working dir
3. copy the hippo data files (oplsaa_forcefield.dat and hippo_protein_database.dat) into the working dir
4. (optional) copy your executable into the working dir
5. start hippo

   hippo

Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time.

If there are problems, look at the log.txt output file.

Steps 1-4 can be automated with the bash script hippo_setup.sh.