# Some questions

بسم الله الرحمن الرحيم

Hello,

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 ?

1. 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 ?

2. 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 3pieta*diameter ( in other program i found 6 instead of 3 what the difference ? )

I set m / damp = 3pietad, therefore damp = m/3pietad

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 ?

Thanks

بسم الله الرحمن الرحيم

Hello,

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 ?

this sounds like an issue with your force field or simulation
parameters. either they are incorrect/unsuitable for your system.
there are far too many details that matter, so it is next to
impossible to help you from remote with this unless there is a big
glaring error. your setup is complex and very specific, so you may
need to approach this in stages and perhaps get some basic experience
with a simpler system first. it is usually best to start with
reproducing well documented examples from literature.

talk to your adviser/supervisor. you need to consult with a local
person with sufficient experience in MD. if that is not available, you
need to join a group with such experience for a month or two.

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 ?

it looks like you need a better understanding statistical
thermodynamics. on the microscopic scale, the _instantaneous_
temperature *always* fluctuates. that the most extreme example: a
harmonic oscillator. at its turning point, all energy is potential
energy, kinetic energy is 0. at equilibrium distance you'll have the
maximum kinetic energy 1/2*m*v^2. on average, it will be half of that.
in a typical simulation system at the microscopic level you have the
equivalent of multiple of those oscillators and they are coupled, too,
so they can transfer energy from one to the other.
overall this leads to a situation similar to having multiple harmonic
oscillators at different force constants, with varying kinetic energy
and different phase. => there will be oscillations and those will be
the larger, the smaller your system is, or get smaller, the larger
your system gets. a "constant" temperature, you will only have in the
limit of an infinite number of particles. however, for a system in
equilibrium, you need not only average over particles, but you can
also average over time. this should give you enough basic information
to look up the details in a text book on statistical thermodynamics
and learn why asking for an exactly constant temperature in an MD
simulation makes no sense.

3. for the damp parameter in fix langevin I do the follwing to include the
viscosity of the water as an implicit solvent;

please note, that this mailing list is not a classroom and we are not
your teaching assistants or your supervisors tasked with checking and