MetaMD simulation is an advanced free energy sampling method which is particularly efficient for rare biological event samplings. Most of the current MD simulation tool support metaMD quite well. However, the speeds for sampling certain collective various (CVs) could be extremely slow. The GPU version of Desmond, developed by David. E. Shaw research, could overcome this limitation and performs MetaMD efficiently.
There are only two CVs are available in Desmond Maestro GUI, namely distances and angles. Other CVs could be specified in the md.msj file as followings:
| CV Description | type | Default width | Wall? | Floor? | Atom sites |
|---|---|---|---|---|---|
| Distance | dist | 0.05 Å | yes | yes | 2 |
| Angle | angle | 2.5° | yes | yes | 3 |
| Dihedral | dihedral | 5.0° | no | no | 4 |
| Radius of Gyration | rgyr | 0.1 Å | no | no | 1 |
| Mass-weighted Radius of Gyration | rgyr_mass | 0.1 Å | no | no | 1 |
| RMSD | rmsd | 0.1 Å | no | no | 1 |
| Symmetry aware RMSD | rmsd_symm | 0.1 Å | no | no | 1 |
| distance along the Z-axis | zdist | 0.05 Å | yes | yes | 1 |
| Absolute distance along the Z-axis | zdist0 | 0.1 Å | yes | yes | 1 |
| WHIM1 | whim1 | 0.5 Å2 | no | no | 1 |
| WHIM2 | whim2 | 0.25 Å2 | no | no | 1 |
You can define a CV site as a single atom or the center of mass of a group of atoms. The site can be defined in terms of ASL expressions, e.g. atom = ["mol.n 2 and not a.e H"], or in terms of atom IDs, e.g. atom = [13 424 92].
Below is an example of a multisim metadynamics stage that defines two collective variables:
simulate {
cfg_file = "config.cfg"
jobname = "$MASTERJOBNAME"
dir = "."
compress = ""
meta = {
cv = [
{atom = ["mol.n 2 and not a.e H"]
type = "rgyr"
width = 0.15
}
{atom = ["(res.num 124 and protein) and not a.e H" "mol.num 2 and not a.e H"]
type = "dist"
width = 0.05
}
]
cv_name = "$JOBNAME$[_replica$REPLICA$].cvseq"
first = 0.0
height = 0.03
interval = 0.03
name = "$JOBNAME$[_replica$REPLICA$].kerseq"
}
checkpt.write_last_step = yes
}
The GPU job of MetaMD could be submitted with the following command:
$SCHRODINGER/utilities/multisim -JOBNAME metaMD -HOST localhost -maxjob 1 -cpu 1 -m meta.msj -c meta.cfg eq-out.cms -mode umbrella -set 'stage[1].set_family.md.jlaunch_opt=["-gpu"]' -o meta-out.cms
One can expect 100-130 ns/day for a typical biological system (50,000-60,000 atoms) with Charmm 36 forcefield on a single Nvidia GTX 980 Ti.
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