Simulaid: utilities for setting up simulations and for the analysis of structures and simulation trajectories.

Simulaid description/documentation: https://mezeim01.u.hpc.mssm.edu/simulaid

To execute Simulaid on Minerva, at the login prompt type
~mezeim01/simulaid/simulaid

For analyzing a single protein structure, download one from the PDB or use one you already have. If there are no hydrogens, add them, e.g., with OpenBabel.

For analyzing trajectories, there is a trajectory and the corresponding structure file in ~mezeim01/molmod_course/md:
~mezeim01/molmod_course/CBP_p53.pdb
~mezeim01/molmod_course/CBP_p53.trj

The trajectory contains 25,000 snapshots. Most analyses are fast (minutes at most). The exception is the generation of the 2D-RMSD.

To run the 2D-RMSD calculation you can gain significant amount of time if you create a new trajectory that

• does not contain the waters
• has only 5000 or less snapshots

• select the output format as Amber (same as the input)
• select atoms to use and ask to drop the solvents
• you can also drop the side chains
• select the first and last frame and the inrement so that yo have fewer than 2900 snapshots (frames)
• go to an interactive node by typing at the prompt
  ssh -X interactive2
  and run the analysis there

Last modified: 11/30/2017

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