Re: [ESPResSo-users] Thermostat, Rigid bond & Rotation feature

[Axel Arnold]

On Tuesday 07 June 2011 09:41:17 Muhammad Anwar wrote:
> Axel Arnold wrote:
> > Hi!
> > 
> > On Wednesday 01 June 2011, Muhammad Anwar wrote:
> >> Hello,
> >> Dear Users & Developers,
> >> I am using espresso-2.2.0b and working on simulation of polymer melt,
> >> first i simulated a system with Lennard Jones particle without any
> >> bonded potential at constant temperature (I put temp 1) using Langevin
> >> thermostat. I calculated the temperature which fluctuate around 1 (0.99
> >> - 1.02) and total pressure is in three digits around 130. Then i added
> >> rigid bond my temperature fluctuate from 0.94 to 0.98 and total pressure
> >> increases to 6 digits around 490000.
> > 
> > Since you don't provide your script, we can only guess. However, the
> > pressure presumably goes up since some particles are constrained at
> > distances with high interaction; you might want to check the pressure
> > components to see which interaction that is. You might want to exclude
> > intramolecular nonbonded interactions, since they are meaningless in
> > case of rigid bonds.
> > 
> >> Then i added cos square bond angle
> >> potential, my temperature fluctuate from 0.64 to 0.69 and pressure again
> >> in 6 digits. Then i added dihedral potential as well and again
> >> temperature  fluctuate from 0.64 to 0.69 and pressure in 6 digits. I
> >> kept epsilon, sigma and other parameters in Lennard Jones and number of
> >> particles same.
> > 
> > If the pressure is too high, probably also some interaction is quite
> > large, which might make it impossible for the thermostat to keep the
> > temperature. Check with a smaller time step, e.g.
> > 
> >> I want to ask what reason might be for smaller value of temperature when
> >> adding bonded potentials and why pressure increases to a big value when
> >> add rigid bonds, does it make sense?
> > 
> > See above.
> > 
> >> Secondly, when i activate ROTATION feature along with rigid bond, i get
> >> the message , currently i can not activate bond constraint and rotation
> >> feature together.
> > 
> > As it says, you cannot use ROTATION with rigid bonds. The reason is that
> > there is no constraints algorithm for rotationally non-invariant
> > particles. If you find a good one, you can try to implement it and
> > contribute to Espresso.
> > 
> > Axel
> 
> Hi,
> Thank very much for your good suggestions, now i want to remove intra
> molecular non bonded interactions. I am using Lennard Jones  non bonded
> interaction, I want monomers of different chains will interact with each
> other with Lennard Jones interactions but monomers of same chains don't
> interact with each other (intra molecular). Before this i defined two
> types of particles for all chains (each chain has two different types of
> particles) and defined Lennard Jones interaction for them.
> Will i need to define different types of particle for each chains (like
> for 1st chain 0,1 types, for 2nd 2,3 and so on) to remove intra
> molecular interactions or is there any simple way? Because in this case
> i will need to define interaction hundreds of time as number of chains
> will increase.

No, this is commonly known as exclusions in MD codes, and also exists in 
Espresso. Take a look at the Users' guide on the part ... exclude  command.

Axel

-- 
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609