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

[Muhammad Anwar]

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.
Thank you very much.

Best Regards,
Muhammad Anwar