Justin A. Lemkul, Ph. Tutorial 1: Lysozyme in Water. GROMACS is free, open-source software, and has consistently been one of the fastest if not the fastest molecular dynamics codes available.
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It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions that usually dominate simulations many groups are also using it for research on non-biological systems, e. The top part of any log file will describe the configuration, and in particular whether your version has GPU support compiled in.
The new neighbor structure required the introduction of a new variable called "cutoff-scheme" in the mdp file. Version These modules can be loaded by using a module load command with the modules as stated in the second column in above table. For example:. These versions are also available with GPU support, albeit only with single precision. In order to load the GPU enabled version, the cuda module needs to be loaded first.
The modules needed are listed in the third column of above table, e. For more information on environment modules, please refer to the Using modules page. Commonly the systems which are being simulated with GROMACS are so large, that you want to use a number of whole nodes for the simulation.
Please see section Performance Considerations below. In order to run a simulation, one needs to create a tpr file portable binary run input file. This file contains the starting structure of the simulation, the molecular topology and all the simulation parameters.
Tpr files are created with the gmx grompp command or simply grompp for versions older than 5. Therefore one needs the following files:. Tpr files are portable, that is they can be grompp' ed on one machine, copied over to a different machine and used as an input file for mdrun. One should always use the same version for both grompp and mdrun.
Although mdrun is able to use tpr files that have been created with an older version of grompp , this can lead to unexpected simulation results. MD Simulations often take much longer than the maximum walltime for a job to complete and therefore need to be restarted.
To minimize the time a job needs to wait before it starts, you should maximise the number of nodes you have access to by choosing a shorter running time for your job.
Requesting a walltime of 24 hours or 72 hours three days is often a good trade-off between waiting- and running-time. This causes mdrun to create a new checkpoint file at this final timestep and gives it the chance to properly close all output-files trajectories, energy- and log-files, etc. You can restart a simulation by using the same mdrun command as the original simulation and adding the -cpi state.
Mdrun will by default since version 4. GROMACS will check the consistency of the output files and - if needed - discard timesteps that are newer than that of the checkpoint file. Using the -maxh parameter ensures that the checkpoint and output files are written in a consistent state when the simulation reaches the time limit. There is no "One size fits all", but the best parameters to choose highly depend on the size of the system number of particles as well as size and shape of the simulation box and the simulation parameters cut-offs, use of Particle-Mesh-Ewald  PME method for long-range electrostatics.
This section often contains notes on how to further improve the performance. Parallel scaling is a measure how effectively the compute resources are used. It is defined as:. This works well until the time needed for communication becomes large in respect to the size in respect of number of particles as well as volume of the domain.
In that case the parallel scaling will drop significantly below 1 and in extreme cases the performance drops when increasing the number of domains. GROMACS can use Dynamic Load Balancing to shift the boundaries between domains to some extent, in order to avoid certain domains taking significantly longer to solve than others.
The mdrun parameter -dlb auto is the default. The Particle-Mesh-Ewald method PME is often used to calculate the long-range non-bonded interactions interactions beyond the cut-off radius.
The mdrun parameter -npme can be used to select the number of PME ranks manually. Mdrun will attemtp to do that automatically since version 4. However for jobs running on a very large number of nodes it might be worth trying even larger number of cpus-per-task. When that is the case, the smallest common denominator is used.
This means that you may end up with a suboptimal choice of kernel function, depending on which compute nodes the scheduler allocates for your job. For example, a simple job script could look like the following:. However, you should also consider that restricting yourself to only AVXcapable nodes will result in longer wait times in the queue.
PLUMED  is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.
Development of that tool seems to have stalled in April and no changes have been made since then. Therefore it is only compatible with Gromacs 5. Biomolecular simulation. Jump to: navigation , search. Translate this page. Other languages:. More content for this section will be added at a later time.
Tips how to use GPUs efficiently will be added soon. Message Passing Interface. GNU Compiler Collection, an open source compiler collection. Intel Math Kernel Library, a software library of optimized math routines.
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Gromacs User Manual Version 4.6