domainswap¶
Parameters controlling a domain swap TMD simulation
Single-valued attributes:
cpu-override: revert to cpu version of namd3 since GPUresident namd3 cannot handle restraints (yet) (default: True)
swap_domain_def: VMD atomselect string for the domain; will be appended with “and chain X” for each chain
anchor_domain_def: VMD atomselect string for the anchor domains; will be appended with “and chain X” for each chain
chain_directional_swaps: list of pairs of directional swaps of chainIDs [[A,B], [B,A]] swaps A and B
force_constant: force constant used in biases for domain-swap CV MD simulation (200) (default: 200.0)
target_numsteps: number of timesteps to run the biased MD simulation (default: 10000)
nsteps: number of timesteps to run the biased MD simulation (default: 10000)
dcdfreq: number of timesteps between dcd output (default: 100)
xstfreq: number of time steps between cell size output to DCD file (default: 100)
temperature: temperature of thermostat in MD run (default: 300)
ensemble: ensemble in which MD is run [NVT] (default: NVT)