A simple dissipative particle dynamics code written in C#
Note: this document is obviously incomplete at this stage!
This code implements a version of the dissipative particle dynamics (DPD) approach of Hoogerbrugge and Koelman, with a particular emphasis on the application of DPD to the study of self-assembling lipid systems after Venturoli and co-workers [1] [2].
In principle, anything that supports .NET Core!
For a quick and simple test, run the provided example.dpd simulation:
dotnet run -c Release example.dpd
On my machine, this produced the following (partial) output:
DPD simulation parameters:
step_no is 1
max_steps is 25000
save_every is 1000
print_every is 1000
delta_t is 0.01
ran1 initialised with -1
rcut is 1
lambda is 0.65
sigma is 3
kBT is 1
cell is 10, 10, 10
3 site types:
w; (internal 0)
h; (internal 1)
t; (internal 2)
2 molecule types:
lipid; 115 counts in system:
13 sites
h, (id 1)
h, (id 1)
h, (id 1)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
t, (id 2)
12 bonds
1 - 2 : eq length 0.700, k 100.000
2 - 3 : eq length 0.700, k 100.000
4 - 5 : eq length 0.700, k 100.000
5 - 6 : eq length 0.700, k 100.000
6 - 7 : eq length 0.700, k 100.000
7 - 8 : eq length 0.700, k 100.000
9 - 10 : eq length 0.700, k 100.000
10 - 11 : eq length 0.700, k 100.000
11 - 12 : eq length 0.700, k 100.000
12 - 13 : eq length 0.700, k 100.000
3 - 4 : eq length 0.700, k 100.000
3 - 9 : eq length 0.700, k 100.000
8 angles
1 - 2 - 2 : eq length 3.142, k 20.000
3 - 4 - 4 : eq length 3.142, k 20.000
5 - 6 - 6 : eq length 3.142, k 20.000
5 - 6 - 6 : eq length 3.142, k 20.000
7 - 6 - 6 : eq length 3.142, k 20.000
7 - 8 - 8 : eq length 3.142, k 20.000
9 - 10 - 10 : eq length 3.142, k 20.000
11 - 10 - 10 : eq length 1.571, k 3.000
water; 1505 counts in system:
1 sites
w, (id 0)
0 bonds
0 angles
3 interactions (defined in kBT):
w h t
w 25.000 15.000 80.000
h 15.000 35.000 80.000
t 80.000 80.000 25.000
3000 sites
Friction coefficient is 4.5 ( as sigma = 3 )
Bead density is 3 per cubic Rc
Step 1/25000, sim time 0.01, CPU time 0s:
Total energy : 82611.000952
Kinetic energy : 0.000000 ( Average 0.000000, target kBT 1.000000, current kBT 0.000000
Nonbonded energy : 17012.909054 ( Average 0.667697 from 25480 collisions )
Bond energy : 63770.842239 ( Average 23.105378 )
Angle energy : 1827.249659 ( Average 0.662047 )
Pressure : 31750.091898 -74.144343 -979.841738
382.087685 26738.832904 -11612.713943
-895.692263 -11612.713943 -134962.321490
System centre of mass = -0.371813 -0.536461 -0.466457
Net system momentum = 0.000000 0.000000 0.000000
Step 1000/25000, sim time 10.00, CPU time 13s:
Total energy : 18461.168546
Kinetic energy : 5035.358600 ( Average 1.678453, target kBT 1.000000, current kBT 1.118969
Nonbonded energy : 11588.845911 ( Average 0.697325 from 16619 collisions )
Bond energy : 1000.591255 ( Average 0.362533 )
Angle energy : 836.372780 ( Average 0.303034 )
Pressure : 25.097875 0.023494 -0.262328
0.737263 22.137103 -0.039258
0.494367 -0.039258 22.651976
System centre of mass = 0.044853 -0.043127 0.040210
Net system momentum = 0.000000 0.000000 0.000000
After a few thousand timesteps, the system should move from disorder to form a lamellar lipid bilyer membrane system (Fig. 1, lipid "tails" are gray, lipid "head" region is blue, water not shown).
- The PDB file written by
gen_system.pyactually contains the system coords scaled by 10. This is to avoid problems with e.g. VMD inferring bond information from distances between particles rather than using theCONECTentries in the PDB file. The coordinates etc in the actual DPD sim file are unscaled. - The use of
UnwrapTrajectoriesfrom MolecularUtilities can prove to be very useful in visualizing the output, to ensure bonds do not "wrap" across periodic boundaries resulting in a visual mess.