Molecular Dynamics

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 Ascalaph Designer, 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

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 Tune button (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 and Start 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 .

Supercomputer Calculations

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 MDynaMix instructions.

Analysis of results

The trajectories obtained by molecular dynamics simulations are analyzed by the Tranal utility of the MDynaMix package (consult the Tranal documentation).