DHFR (dihydrofolate reductase) is a globular protein commonly used as a benchmark in MD simulations.
For the MD simulation with ACEMD3, you need:
Prepare the simulation system and corresponding force field files
Write an input file
Run the simulation
In this tutorial, we show how to run the MD simulation with ACEMD3 directly:
ACEMD3 installation already contains files for the DHFR simulation with CHARMM 36 force field. Copy them to an empty directory:
$ cd /tmp $ cp -r $(dirname $(which acemd3))/../share/acemd3/dhfr_charmm . $ cd dhfr_charmm
The input file is for an NVT (298.15 K) simulation with 4 fs time step:
$ cat input parameters dhfr.prm structure dhfr.psf coordinates dhfr.pdb celldimension 62.23 62.23 62.23 thermostat on run 250000
The other parameters are set to the default 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 different GPU.
During 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):
$ ls -1 dhfr.pdb dhfr.prm dhfr.psf input output.coor output.vel output.xsc output.xtc restart.chk
ACEMD3 is a substantial development over the previous version (i.e. ACEMD). The main changes affecting users:
Simplified input file
Discontinued TCL scripting
If you are using ACEMD directly, the migration needs some work: