Welcome to the HECBioSim download repository, you will find tools and software that we make available here. If you would your software/tool/script to be distributed here, then please get in touch and we can arrange for you to made a contributor.

 

archive.png FESetup 1.2.1

(36 votes)

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A tool to automate setup for alchemical relative free energy simulations with Molecular Dynamics and Monte Carlo, and a tool for general simulation setup like equilibration.

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2,943
91.3 MB
GNU/GPL external

 

 

longbow.png Longbow v1.5.1

(26 votes)

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Longbow is our remote job submission and management tool. Longbow is designed to work out of the box for biomolecular simulation packages (AMBER, CHARMM, GROMACS, LAMMPS, NAMD) on HPC's that operate on LSF, PBS, SGE or SLURM schedulers. Longbow is not limited to these packages alone, an interface is provided to allow users to extend Longbow to work with other schedulers/software packages.

This package is intended for users that chose to not install via the pip installer.

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3,384
80.94 KB
BSD-3 Clause external

 

 

longbow.png Longbow - Examples v1.5.x

(6 votes)

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This download contains the examples for the Longbow job submission tool. This package is intended for users that wish to not use the below command but wish to obtain a copy manually.

 

% longbow --examples 

 

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4,923
17.18 MB
BSD-3 Clause external

 

 

bench.png HECBioSim Benchmarks for AMBER 1.0.0 NEW

(0 votes)

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These benchmarks form part of the HECBioSim benchmark suite for the AMBER MD software package. The systems contained within this suite are explained here.

If you have any problems running these benchmarks then please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for support.

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67
241.92 MB

 

 

bench.png HECBioSim Benchmarks for GROMACS 1.0.0 NEW

(0 votes)

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These benchmarks form part of the HECBioSim benchmark suite for the GROMACS MD software package. The systems contained within this suite are explained here.

If you have any problems running these benchmarks then please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for support.

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80
106.25 MB

 

 

bench.png HECBioSim Benchmarks for LAMMPS 1.0.0 NEW

(0 votes)

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These benchmarks form part of the HECBioSim benchmark suite for the LAMMPS MD software package. The systems contained within this suite are explained here.

If you have any problems running these benchmarks then please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for support.

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65
409.03 MB

 

 

bench.png HECBioSim Benchmarks for NAMD 1.0.0 NEW

(0 votes)

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These benchmarks form part of the HECBioSim benchmark suite for the NAMD MD software package. The systems contained within this suite are explained here.

If you have any problems running these benchmarks then please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for support.

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67
343.71 MB

 

 

archive.png cpptraj mod for AmberTools 13

(2 votes)

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The cpptraj routines, a brief description can be found here. Users with questions or requiring support with this should contact Hannes Loeffler This email address is being protected from spambots. You need JavaScript enabled to view it. 

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1,146
1.01 MB

 

 

archive.png ptraj mod for AmberTools 13

(2 votes)

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Extension for ptraj to include some useful new routines. More information about this download can be found here. There is also a brief description of how to compile it into AmberTools at the aforementioned link. 

For more support or more information about this software please contact Hannes Loeffler This email address is being protected from spambots. You need JavaScript enabled to view it.

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1,148
413.67 KB