بسم الله الرحمن الرحيم
I have some questions which are:
1. I am using fene/expand without LJ terms ( set epsillon and sigma equal to zero ) as bond_style in my simulation, but there are errors which are too long fene bond and bad fene bond. I know that fene potential has a boundaries that the bonded atoms must not exceed them, but in my simulation there are a two pair_style which are coul/debye and morse and these pairs produce large repulsive ( same charge in coul ) forces when the distance between the atoms becomes small and small and this leads to increase the distance between atoms especially the bonded ones. therefore producing the problem of the fene potential.
How I can solve this problem ?
2. I am using fix langevin with fix nve to perform a Brownian dynamics and I set Tstart equal to Tstop equal to 298.15 ( 25 C ) and the damp equal to 39.4, but when the simulation run the temp. varies and I need it to be fixed, so how can I fix it ?
3. for the damp parameter in fix langevin I do the follwing to include the viscosity of the water as an implicit solvent;
the coeff of the drag focre is m / damp and in BD the coeff is equal to 3*pi*eta*diameter ( in other program i found 6 instead of 3 what the difference ? )
I set m / damp = 3*pi*eta*d, therefore damp = m/3*pi*eta*d
I put m ( mass of the beads in my simulation = 0.113 kg/mole
eta = 0.00089 kg/m.s for water
d ( for the bead ) = 5.68e-10 m
the unit of the answer is s/mole
I divide the answer by Avogadro's number and get 39.4 fs ( unit of time for real )
is this correct for BD in water ?