MDEnergy - energy evaluation tool
Introduction
MDEnergy is a program to calculate energies from DCD or PDB-files. It
is originally derived from
Mindy, a simplified
version of the
NAMD engine,
written by Justin Gullingsrud.
It can calculate the different bonded and
nonbonded energies for each atom based on the information from the PSF-file
and the coordinate file that you have to specify. The total energy values
are identical to the NAMD output, except for roundoff errors in case you
specify the same cutoff and switch distance as in the NAMD input file.
You can also compute the energy for a selection of atoms or determine
the interaction energy between two sets of atoms.
MDEnergy is very memory efficient because is processes DCD files frame
by frame. The output format is similar to NAMD's output and you can plot
it with 'namdplot' (comes with NAMD).
Contact
If you have questions please send email to the author Jan Saam,
at
saam@charite.de
or
saam@ks.uiuc.edu.
Download
License
Same terms as NAMD license
Documentation
The TCL-script visual_mdenergy.tcl contains a procedure with the same name that
visualizes the atom based energy values. You must use the mdenergy
option -a to dump the atom energies to a file that can be read by
visual_mdenergy.
You must specify on the command line or in the wrapper srcipt:
--------------------------------------------------------------
You always need a PDB or DCD file as coordinate input:
-pdb file and/or
-dcd file : You can specify as many files as you want, they will
process in order of occurance. They must have the same
number of atoms and MDEnergy assumes that they all belong
to the same structure.
And you need parameters and structure information:
-par file : The parameter file in charmm style.
or
-xplor file : The parameter file in xplor style.
-psf file : The PSF file (charmm/xplor).
or alternatively
-amber : AMBER partop file (parm7)
(contains parameters and structure)
You must specify one or more of the following options to tell mdforce
which energies it has to calculate:
---------------------------------------------------------------------
-smooth n : No energies are computed but a trajectory with smoothed
coordinates is emitted. See -avg for info how smoothing
works.
-all : All energies are computed
-bond : Bond energy
-angl : Angle energy
-dihe : Dihedral energy
-impr : Improper energy
-vdw : Van der Waals energy
-elec : Electrostatic energy
-nonb : Nonbonded energies (elec, vdw)
-conf : Conformational energy (bond, angl, dihe, impr)
-kin : Kinetic energy (need velocity dcd file: -vel file)
-hbon : Computes h-bond energies (angle and distance dependent)
which can be very nicely visualized in VMD with the script
visual_hbonds (in 'hbonds.tcl'). See documentation therein.
You need to have:
A psf file with populated NBON and NACC fields to tell
MDEnergy about the donors and acceptors in your system.
You can generate it using the 'hbondpsf' tool which is
contained in this distribution. With the help of the
DONOR/ACCEPTOR information in the topology file and an
existing psf file it generates a new psf including the
required donor/acceptor info.
-hpar file : h-bond parameter file
A sample file that should be sufficient for
most cases is provided in hbonds/hpar
Optional:
-pat file : If there are patches in the molecule, then
specify them in a file in th same format as
you would do for 'psfgen'.
POOR DOCUMENTATION, I KNOW!
ASK ME WHEN YOU NEED THIS FEATURE.
ther options/parameters:
-------------------------
-xplor : By default MDEnergy assumes a CHARMM format parameter file.
Use this option to tell MDEnergy that you are using xplor
format.
-beg n : the first frame to process. Default=0
-end n : the last frame to process. you can say 'last' instead of a
number, if you just mean the last frame of the dcd file.
Default='last'
-switch : switch distance for VDW interaction. Default=10
-cutoff : cutoff distance for nonbonded calculation. Default=12
(switch is the distance at which the switching function for VDW
interaction begins, cutoff is where it ends and where the VDW
interaction is zero.
-switch 20 -cutoff 25 starts the switching function at 20A and
at 25A it has reached zero.
For the electrostatic interaction switch has no meaning, while
cutoff marks the point where the interaction is zero. The
potential function is shifted to obtain this.)
-scale14fac n : VDW 1-4 scaling factor in CHARMM style
-sncb n : VDW 1-4 scaling factor in AMBER style.
This would be 1/scale14fac. See NAMD manual for details.
-noamberexcl : Don't read exclusions from parm file but autogenerate
them.
-sel file : File with indices for an atom selection.
The energy for the selected atoms is computed.
For the nonbonded energies the interaction of the selection
with the environment is included.
If this option is used twice the nonbonded interaction energy
between the two selections is computed.
-self : If you have specified a selection with -sel then the
nonbonded energies are computed only within the selection.
Otherwise the interaction with the environment (but not the
self energy of the environment) is included.
-diel n : Dielectric constant. This only makes sense if you want to
calculate the interaction between two sets of atoms. You can
use it for simple docking experiments between two molecules.
If you don't have water between them you could for example
specify -diel 80. Note that this is a rather rough method.
It assumes the dielectric constant for the entire space
between the atoms of the two selections, even if there are
other parts of the protein or the selection itself between
them.
-a file : Dumps energies for all individual selected atoms into a file
which can be read by the script 'viz_energy.tcl' to visualize
the energy contributions per atom in VMD.
Use one energy type option only!
File format (entries line by line):
# header
1) energy type
2) number of atoms
3) selection text
4) atom index list of the selection
# body (for each frame)
1) frame number
2) indexes of min and max values for current frame
3) min and max energy values for current frame
4) A long line containing the energy values for each atom
-log : The energy output will be on logarithmic scale. This can be
useful for visualization.
-avg n : You can get running averages of all output by specifying this
option. The width of the symmetric sliding average window is
2n+1. This effects the total energy output on the screen as well
as well as the values for the individual atom dumped into a file
by '-a file'.
By default your output size is reduced by 2n frames, n frames
missing at the beginning and the end. This is because the average
has to be build up. Use options -pad or -ramp to preserve the
number of frames.
-pad : To be used with -avg. The missing frames at the beginning and
the end are padded with the first averaged frame.
-ramp : To be used with -avg. The missing frames at the beginning and
the end are replaced by ramping the average up and down. That
means the averaging window is not symmetric and has not the
same size at the ends but the average is computed from as all
available frames. This gives smoother looking results at both
ends.
VMD-PLUGIN
==========
The VMD scripts energy.tcl and interact.tcl contain procedures
'energy' and 'interact' which are calling a shell script 'runvmdenergy'
that determines which binary of MDEnergy to run. Binaries exist for
Linux, Solaris and Irix.
MDEnergy runs as a background process so you can continue with your
work in VMD. The output is similar to NAMD's output and you can plot
it with 'namdplot' (a tool which is part of the NAMD distribution).
MDENERGY.TCL
----------------------------------------------------------------------
This script is an interface to compute energies conviniently in VMD.
Usage:
mdenergy -bond|-angle|-dihed|-impr|-vdw|-elec|-nonb|-all -sel $sel [$sel2] [opti
ons]
!!! SEE THE HEADER OF THE SCRIPT FOR MORE DETAILED DOCUMENTAION !!!
