Molecular dynamics calculations are carried out by the internal methods
(menu Compute > Dynamics) or by the external program
(menu Tools > MDynaMix).
Supercomputing on PC
In 2007, NVIDIA introduced video cards
that could be used not only to show graphics but also for scientific calculations.
These cards include many arithmetic units (currently up to 240) working
in parallel. Long before this event, the computational power of video cards
was used to accelerate calculations. What was new is that NVIDIA made it possible
to develop parallel programs in a high-level language.
Actually, it is the C language supplemented with several key words.
This technology called CUDA
substantially simplified programming by introducing the CUDA code in programs
written in на C/C++.
Ascalaph Liquid GPU
is a hardware accelerated version of
identical in all features except performance.
It requires special hardware and software.
The program uses an NVIDIA card to speed up the computation of non-valent interactions.
MDynaMix is an independent
console application for molecular dynamics simulations. It was written in
Fortran 77 and can run across many platforms (including clusters of
workstations supporting parallel computing using MPI).
The graphical shell does not allow full access to the application's features. In particular, presently parallel
computing is not supported. The interface helps to construct models, associate them with
a force field, and prepare everything required for simulation. The proper simulation can be started
from the graphical interface or as a console application. In the later case simulation can be manually
transferred to a parallel computer. A mixed protocol is possible when the model is constructed using
the graphical interface, modified outside of it, and started from the graphical interface
(see the Tune/Start versus Run section).
The MDynaMix panel sets most routine options. Note the
Read restart option in the Restart control section.
Checking this option forces the simulation to use the atomic rates and periodic box size from
the previous calculation rather than those specified in the panel.
Starting the molecular dynamics algorithm by the Run button
or pressing the
(see below) forces the interface to generate all files required for
the console application.
If the simulation is interrupted by pressing the Stop button,
the MD_STOP file is generated. If this file is present, the
console application immediately stops. Make sure that no such file is present when manually
starting the console application.
Tune/Start versus Run
If the options provided by the graphical interface are not sufficient or the files generated
by should be modified, the combination of the Tune
buttons can be used. Pressing the Tune
button will generate all files required for the simulation (which is also done after pressing
the Run button) but the console application is not executed.
At this point, any files can be modified. Pressing the Start button
runs the console application without generating any files.
The Tune + Start combination is
similar to the Run button
MDynaMix allows parallel computing on supercomputers and clusters of workstations.
The graphical interface can be used to generate input data for such computing. A model can be constructed
and a short molecular dynamics simulation can be performed to confirm its validity under the graphical
shell and then transferred to a powerful computer. The control and input data files can be generated
by pressing the Tune button. In this case, the interface performs all tasks
preceding MDynaMix execution but it will not start. The following files are generated:
- MDynaMix.input file with control parameters;
- MDynaMix.start file with atomic coordinates;
- moldb/~<molecular formula>.mmol files describing the molecules (except for the water molecule).
To start the task on a cluster of workstations, these files should be copied to it. The
Visual option should be changed from yes
to no in the MDynaMix.input file,
while all other files remain unaltered. The files describing the molecules are located in the
moldb folder and start with a '~' sign; they should be transferred
to a similar folder on the cluster of workstations. If water is used in the simulation, the
H2O.mmol file should also be transferred. It is the only
mmol file not generated by the graphical interface and it does not
start with a '~' sign. The subsequent task execution and control are performed according to the
Analysis of results
The trajectories obtained by molecular dynamics simulations are analyzed by the
Tranal utility of the MDynaMix package (consult the