DHFR (dihydrofolate reductase) is a protein commonly used as a benchmark in MD simulations.
For the simulation, you need:
All these tasks can be done easily with HTMD: follow the tutorial of the molecular dynamics protocols.
Alternatively, you can run the simulation with ACEMD3 directly:
Download already prepared files for the DHFR simulation with CHARMM 22 force field:
An input options for NVT (298.15 K) simulation:
parameters par_all22_prot.prm structure dhfr.psf coordinates dhfr.pdb celldimensions 62.23 62.23 62.23 temperature 298.15 thermostat on thermostatTemp 298.15 run 100ns
Save it to an
By default, ACEMD3 uses 4 fs time step and applies necessary constraints automatically.
The other simulation parameters are set the standard values (see the input file options for details).
Start the simulation:
$ acemd3 input
By default, ACEMD3 runs on the first GPU (device 0).
This can be changed with
--device argument (see the command line arguments for details).
Note that ACEMD Pro licence is required to run on all GPUs.
During the course of the simulation, log messages are written to the standard output and simulation trajectory is saved to
Also, the simulation state is periodically saved to
restart.chk (see the input options for details).
ACEMD3 is a substantial development over the previous version (i.e. ACEMD). The main changes affecting users:
If you are using ACEMD directly, the migration needs some work: