1. Analyzing MD Results

2. Extracting system properties from the data written to the mdout files MD information is written in the form: NSTEP = 100 TIME(PS) = 10.200 TEMP(K) = 297.23 PRESS = -1257.4 Etot = -73238.8859 EKtot = 18131.6434 EPtot = -91370.5294 BOND = 654.2822 ANGLE = 1929.4666 DIHED = 775.1417 1-4 NB = 817.8912 1-4 EEL = 4242.6763 VDWAALS = 9440.1805 EELEC = -109230.1680 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 7732.1695 VIRIAL = 16916.4636 VOLUME = 338304.5955 Density = 0.9012 Ewald error estimate: 0.1550E-03 ------------------------------------------------------------------------------ To extract it for plotting one may use a Perl script, process_mdout.perl, available from the Amber Tutorial page

3. Extracting system properties from the data written to the mdout files One needs to analyze several system properties to ensure system reached equlibrium Relaxation Equilibrium

4. Extracting system properties from the data written to the mdout files Not all system properties reach equilibrium at the same time

5. Analyzing the trajectory Program ptraj is a main tool for analyzing sets of 3-D coordinates read in from a series of input coordinate files in various formats. To use the program it is necessary to (1) read in a parameter/topology file; (2) set up a list of input coordinate files; (3) optionally specify an output file and (4) specify a series of actions to be performed on each coordinate set read in.

6. Analyzing the trajectory Calculating RMSD from the reference structure

7. Analyzing the trajectory Calculating RMSD from the reference structure Input file for ptraj: trajin 1cgh-equilib-md.mdcrd.gz  You can use gzipped trajectories reference 1cgh-all-minimize.rst  Reference Structure rms reference out 1cgh-backbone.rms @C,N,CA time 1  We want to calculate RMSD for all atoms with names C, N, and CA (protein backbone atoms) and to save result into file 1cgh-backbone.rms ptraj topology_file <input_file  Command to run ptraj