Open susilehtola opened 1 year ago
We encountered this issue in metadynamics on the vanillin molecule with the coordinates
$coord
-3.14393748772232 3.33813352345031 -0.00014119336956 o
7.86002766715000 -1.65701448465138 0.00040621434150 o
5.74049590710396 -2.49527551648547 -0.00050479923313 c
3.42304695453588 -0.98774709392443 -0.00010485496334 c
1.06591048798478 -2.15083142745214 -0.00014844660978 c
-1.17270680517221 -0.77415535108070 -0.00013844779300 c
-3.30174527376127 -2.20634525593637 -0.00025807238808 o
-5.72053722271011 -1.08375306666073 -0.00010984349014 c
-1.01555970570177 1.88182884434437 -0.00005730429937 c
1.35264373756029 3.03267846294878 0.00013226089640 c
3.55184020306940 1.64453015125235 0.00021056287264 c
-2.66751301607659 5.09916430174068 -0.00002324857945 h
5.40066653268587 -4.56215905836274 0.00078445601463 h
0.91214108164020 -4.18420996464937 -0.00021662002928 h
-7.04162340875582 -2.66213089601776 -0.00034302738473 h
-6.02711939534645 0.06913218178066 1.68326359513705 h
-6.02710355274802 0.06966531366495 -1.68313322383375 h
1.43463686418473 5.07677471557364 0.00015134556396 h
5.37644021153172 2.55171839991760 0.00024009577804 h
$end
and the input
$md
temp=300
time=10.0
dump=5.0
step=0.5
shake=0
$end
$metadyn
save=10
kpush=1.0
alp=0.2
$end
The result does not appear to be fully reproducible, though. I wonder if another issue is that atoms can be placed on top of each other in the random initialization.
For instance, running
xtb --omd --input metadyn.inp coord
on my laptop with xtb-6.5.1-1.fc37.x86_64
I got the following result
time (ps) <Epot> Ekin <T> T Etot
0 0.00 0.00000 0.0613 0. 0. -33.29787
est. speed in wall clock h for 100 ps : 0.36
200 0.10 -32.60311 0.3225 1967. 3573. -32.42622
400 0.20 -32.71420 0.3797 3016. 4207. -32.48540
600 0.30 -26.03888 0.3612 3399. 4002. 0.36117
800 0.40 -19.53728 0.3006 3463. 3330. 0.30058
1000 0.50 -15.63373 0.2510 3379. 2781. 0.25098
1200 0.60 -13.03028 0.2104 3241. 2331. 0.21038
1400 0.70 -11.17014 0.1771 3084. 1963. 0.17714
1600 0.80 -9.77474 0.1499 2924. 1661. 0.14992
1800 0.90 -8.68926 0.1276 2770. 1414. 0.12764
2000 1.00 -7.82077 0.1094 2624. 1212. 0.10941
after which xtb crashed. However, other runs worked fine.
The biasing potential in metadynamics is controlled by the MD step number. This means that the biasing potential gets switched on instantaneously when a small time step is used, resulting in the system exploding. For instance, when running systems with hydrogens with
shake=0
and the usual 0.5 fs time step, one experiences an explosion already in the initial dynamics run since the starting configuration is included in the metadynamics potential.The correct way to switch on the biasing potential is to do it as a function of actual time.