Transcript Amber9 Simple Analysis

Analyzing MD Results
Extracting system properties from the
data written to the mdout files
MD information is written in the form:
NSTEP =
Etot
BOND
1-4 NB
EELEC
EKCMT
100
TIME(PS) =
-73238.8859 EKtot
654.2822 ANGLE
817.8912 1-4 EEL
-109230.1680 EHBOND
7732.1695 VIRIAL
10.200 TEMP(K) =
297.23 PRESS = -1257.4
=
=
18131.6434 EPtot
=
-91370.5294
=
=
1929.4666 DIHED
=
775.1417
=
=
4242.6763 VDWAALS
=
9440.1805
=
=
0.0000 RESTRAINT =
0.0000
=
=
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
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
Extracting system
properties from the data
written to the mdout files
Not all system properties reach
equilibrium at the same time
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.
Analyzing the trajectory
Calculating RMSD from the reference structure
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