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bio-ESMD (biological Exa-Scale Molecular Dynamics) is a biological system simulation software for Sunway Processors. Which is build on the top of ESMD. ESMD and bio-ESMD are implemented with cell lists, which can make full use of the DMA and GLD/ST bandwidth, then we have change to optimize the computation part.
bio-ESMD uses GNU Make for compiling, on generic multi-core processors, the only dependency is MPI.
For Sunway:
The Makefile can detect the architecture of Sunway automatically.
With swgcc710-5A:
module load sw/compiler/gcc710 cd qthread make target=5 cd ../src make
The executable will be generated in bin/esmd
bio-ESMD is released with two test cases, the command line arguments are:
./esmd <config file>
For example:
./esmd ../ubq_wb/ubq_wb_eq.conf
Suggested bsub parameters on the TaihuLight are:
bsub -I -q <your_queue_name> -share_size 6144 -host_stack 16 -b -cgsp 64 -n 1 -p -sw3run swrun-5a ../bin/esmd <your_conf_file>
Currently the checkpoint is not supported.
Supported parameters in config file includes:
| Parameter | Format | Description |
|---|---|---|
| root | Path | Specify the path for ESMD to read file, $WORKDIR current working dir, $CONFDIR for config file dir |
| coordinate | Path to a PDB file | Coordinates of the molecule |
| structure | Path to a TOP file | Topology of the molecule (in GROMACS format) |
| parameters | Path to a parameter file | This option is deprecated |
| rcut | real | Cut-off radius |
| rswitch | real | Switch radius |
| coulscaling | real | Coulomb scaling factor for 1-4 scaling. |
| cell | real | the bounding box for the unit cell xlow ylow zlow xhigh yhigh zhigh
|
| msmlevels | int[3] | MSM levels in three dimensions |
| msmorder | int | the MSM order |
| coulconst | real | |
| dt | real | timestep size |
| nsteps | int | number of timesteps |
| trajectory | Path | prefix for the trajectory file |
| trajfreq | int | number of timesteps between trajectory output |
| rigidtype | shake/lincs/none | specify the rigid bodies constraint algorithm |
| rigids | string | DISABLED |
| coultype | rf/shifted/msm | Coulobm algorithm, RF for reaction field, currently eps-rf=78.5 |
| temperature | real | initial temperature in K |
| tempcouple | nh/none | temperature coupling algorithm, only nh or none acceptable. |
| tempstart | real | starting temperature |
| tempstop | real | ending temperature |
| tempchain | int | length of Nose-Hoover Chains |
| minimize | int | number of minimization steps. |
| rigidscale | real | We use stiff bond condition for minization with rigid bodies, that is, the bonded energy is multiplied by this number if the bond is a rigid body. |
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