Re: [ESPResSo] Position-dependent Langevoin thermostat

[Lorenzo Isella]

Hello,
Thanks for the many replies. I think I am now in a condition to ask a
few questions (before perhaps moving this to the developer mailing
list, you will tell me what you think it is appropriate for me to do).
Let me briefly list the important points for what I am planning to do:
(1) I want to make each monomer in a cluster (i.e. individual particle
I create in espresso) aware its first neighbors (at the very least he
should know how many they are).
I think this is doable since this is (to my understanding) already
implemented in the DPD thermostat, where you can specifiy a cut-off
distance the dissipative and random force. In other words, each
particle knows how many other particles it finds within a distance
r_cut.
(2)Once I have implemented what I have described in (1), then the idea
is to be able to express the friction felt by each individual monomer
as a function of its number of (first) neighbors.The value of the
corresponding noise term should be given again by the
fluctuation-dissipation theorem. Or the other way around: given the
noise term, that should fix the friction.
(3) I would like (in order to be able to investigate the diffusion
coefficient of a cluster) to track simultaneously many trajectories of
copies of the same cluster. For instance: start a simulation with two
clusters A and B. Clusters A and B should be "transparent" to each
other (i.e. the do not feel any reciprocal interaction whatsoever and
each of them can go through the other effortlessly) and for both A and
B I would like to be able to do what described in (1) and (2).

Now, do people on this list think that points (1) to (3) are
achievable? I think I will have to get my hands "dirty" by modifying
espresso source code, but I will have at the very least to ask some
technical questions (and not all of them at the highest level; my
programming skills are probably on a different league wrt many people
on this list).
Bottom line: before embarking in all this, any comment/suggestion is
more than welcome.
Kind Regards

Lorenzo




2008/9/17 Christoph Junghans <address@hidden>:
> Hi Lorenzo & Olaf,
>
> there is no problem in modifying the langevin thermostat as long as you keep
> the ration between noise and friction. In Espresso the noise and friction
> prefactors are saved in langevin_pref1 and langevin_pref2.
> In theory you just have to change them.
>
> From the implementation side this is more complicated, because in Espresso
> there is only one global friction constant for all particles.
> So inside of the function friction_thermo_langevin, you need to know the
> number of neighbors, the position of the aggregate or whatever.
>
> Cheers,
>
> Christoph
>
>