Engines

SSAGES supports multiple molecular dynamics engines. However, supported features between MD engines. This may be the result of engine limitations or work in progress. The table below summarizes the main features that vary between supported engines.

Engine	Supported versions	Multi-walker	NPT virial
LAMMPS	2010 or newer	yes	yes
Gromacs	5.1.x, 2016.3	yes	yes
OpenMD	2.4, 2.5	no	no
Qbox	1.60 or newer	yes	no

Special instructions on how to use SSAGES with a particular engine are listed under the appropriate section.

LAMMPS

Building

SSAGES supports most recent versions of LAMMPS. To compile SSAGES with a compatible version of LAMMPS, either -DLAMMPS=YES or -DLAMMPS_SRC=/path/to/LAMMPS must be specified in the cmake command. For example,

cmake -DLAMMPS=YES ..
make

will automatically download a recent version of LAMMPS (tagged r15407) and compile SSAGES. Because many users may take advantage of optional LAMMPS packages, SSAGES forwards the make commands necessary to do so, such as

make yes-molecule
make yes-user-drude

If a user is interested in using a different version of LAMMPS or one with personal modifications, then SSAGES can be pointed to that particular source repository.

cmake -DLAMMPS_SRC=/path/to/lammps ..

Warning

Once you link SSAGES to a particular LAMMPS source, you will be unable to compile that LAMMPS source outside of SSAGES because of SSAGES dependencies which are introduced. Be sure to backup your repository accordingly.

Running

SSAGES integrates with LAMMPS though the flexible fix API offered by LAMMPS. It is therefore necessary to define a SSAGES fix within the LAMMPS input file as follows.

fix ssages all ssages

This directive ensures that SSAGES is able to locate the appropriate adapter and interface with the LAMMPS library. It is very important to name the fix “ssages” as shown above. Otherwise, SSAGES will not work properly. It is highly recommended that the SSAGES fix command be placed after all integrator fixes. Also, make sure tht the fix is specified before the run command, which will begin the advanced sampling simulation.

Note

Due to the nature of how SSAGES forwards commands to LAMMPS, the use of include within a LAMMPS input script is currently not supported.

SSAGES is compatible with typical LAMMPS workflows that include equilibration or energy minimzation steps before production. So long as the SSAGES fix is not declared, LAMMPS will run without any modification.

The only LAMMPS-specific property required in a SSAGES input file is the input property which points to the LAMMPS input script. Details can be found on the input files page.

Gromacs

Building

SSAGES supports Gromacs versions 5.1.x and 2016.3. To compile SSAGES with a compatible version of Gromacs, either -DGROMACS=YES or -DGROMACS_SRC=/path/to/Gromacs must be specified in the cmake command. For example,

cmake -DGROMACS=YES ..
make

will automatically download Gromacs 5.1.3 and compile SSAGES. If a user is interested in using a different version of Gromacs or one with personal modifications, then SSAGES can be pointed to that particular source repository.

cmake -DGROMACS_SRC=/path/to/gromacs ..

Warning

Once you link SSAGES to a particular Gromacs source, you will be unable to compile that Gromacs source outside of SSAGES because of SSAGES dependencies which are introduced. Be sure to backup your repository accordingly.

Running

SSAGES forwards arguments to the Gromacs mdrun library. The args property must specified in the SSAGES input file as described on the input files page.

OpenMD

Note

Coming soon.

Qbox

Note

Coming soon.