dpd
A program which uses the dissipative particle dynamics (DPD) method to model the dynamics of polymers in explicit solvent.
Current funcionality includes:
- Polymer translocation through a nanopore
- Polymer tethered to a wall
- Free polymer
BUILD:
Compile all.c in the src directory (requires link to math library). Other options in makefile don't currently work (will change this in the future).
RUN:
Run in a directory with input file dpd.inp. Or use sub.sh and run.sh to submit jobs to any Sun Grid Engine system.
INPUT PARAMETERS:
usual/
suggested
variable value type description
Aff 25.0 float Fluid-fluid conservative force strength
Amm 25.0 float Monomer-monomer conservative force strength
Amf 15.0 float Monomer-fluid conservative force strength
sigma 3.0 float Random force strength
gamma 4.5 float Dissipative force strength
K 40.0 float Spring constant for FENE force
fDrive - float Nanopore driving force
Nmon - int Length of polymer chain
density 3.0 float Fluid density
Lx - float System size, x direction
Ly - float System size, y direction
Lz - float System size, z direction
wallDensity 3.0 float density of wallParticles
- Set to <=0 for no wall
wallLayers 2 or 3 int Number of wall particle layers
poreWidth float Nanopore width (square side length)
- Set to <0 for no pore
dt 0.04 float Timestep
tMax - float Simulation time
eqTime - float Time for system to equilibrate
freqSamp - int Sampling freqency for calculated quantities
freqOut 1000 int Print frequency for sampled quantities
ydens 0 1/0 Set to 1 to sample fluid density vs. z
yaveTemp 0 1/0 Set to 1 to sample average temperature
ymonPos 0 1/0 Set to 1 to print monomer positions vs time