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

grading your work.

axel.