Announcing OpenMM command
Posted: Wed Oct 30, 2013 5:17 pm
Hi everyone,
We'd like to announce the OpenMM command - a way for users to run an OpenMM simulation without writing a script. It is analogous to packages such as grompp/mdrun in GROMACS or tleap/pmemd in AMBER.
A few features:
- Sets up your system starting from coordinates and force field.
- Configuration options accessible via command line or configuration file.
- Configuration file is automatically generated for reproducibility.
- Automatic reading and writing of restart files.
- As the program runs, OpenMM scripting commands are printed to screen.
- Real-time reporting of simulation progress, including estimated time remaining and speed in nanoseconds/day.
To run the command, type in something like this:
Output looks like this:
Please download the code and let us know what you think. Ten examples are included, including the joint AMBER-CHARMM benchmark. Please report any issues found through the GitHub issue tracker.
The command is available for download and installation here:
https://github.com/rmcgibbo/openmm-cmd.git
Thanks,
Lee-Ping Wang
Robert McGibbon
We'd like to announce the OpenMM command - a way for users to run an OpenMM simulation without writing a script. It is analogous to packages such as grompp/mdrun in GROMACS or tleap/pmemd in AMBER.
A few features:
- Sets up your system starting from coordinates and force field.
- Configuration options accessible via command line or configuration file.
- Configuration file is automatically generated for reproducibility.
- Automatic reading and writing of restart files.
- As the program runs, OpenMM scripting commands are printed to screen.
- Real-time reporting of simulation progress, including estimated time remaining and speed in nanoseconds/day.
To run the command, type in something like this:
Code: Select all
[color=#0040FF]./openmm --coords dhfr.pdb --protein amber99sb --water tip3p --cutoff 0.9*nanometer --platform CUDA --n_steps 100000[/color]
Code: Select all
[OpenMM] Number of available platforms: 4
[OpenMM] Selected Platform: CUDA
[OpenMM] CudaDeviceIndex = 0
[OpenMM] CudaDeviceName = GeForce GTX TITAN
[OpenMM] CudaUseBlockingSync = true
[OpenMM] CudaPrecision = mixed
[OpenMM] CudaUseCpuPme = false
[OpenMM] CudaCompiler =
[OpenMM] CudaTempDirectory = /tmp
Progress WallTime Left Speed Time P.E.
(%) (d:h:m:s) (ns/day) (ps) (kJ/mol)
0.000% ?? 0.00 0.00000 -297665.03625
1.000% 3:18 86.38 2.00000 -296577.38755
2.000% 3:14 87.10 4.00000 -296647.99384
3.000% 3:11 87.37 6.00000 -296559.64981
4.000% 3:09 87.49 8.00000 -296559.32665
5.000% 3:07 87.59 10.00000 -295607.70956
6.000% 3:05 87.66 12.00000 -297014.37689
7.000% 3:03 87.69 14.00000 -296418.93514
8.000% 3:01 87.71 16.00000 -296663.86197
9.000% 2:59 87.73 18.00000 -297068.98135
10.000% 2:57 87.74 20.00000 -296912.85101
11.000% 2:55 87.75 22.00000 -296909.89700
12.000% 2:53 87.77 24.00000 -296276.15998
13.000% 2:51 87.78 26.00000 -296437.97360
14.000% 2:49 87.78 28.00000 -297273.77364
15.000% 2:47 87.79 30.00000 -297464.42631
16.000% 2:45 87.80 32.00000 -297623.40073
17.000% 2:43 87.81 34.00000 -296831.45315
The command is available for download and installation here:
https://github.com/rmcgibbo/openmm-cmd.git
Thanks,
Lee-Ping Wang
Robert McGibbon