I have a little doubt over the damp in fix langevin. We know the syntax :
fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
I came across the following lines in the manual :
"The damp factor can be thought of as inversely related to the viscosity of
the solvent. I.e. a small relaxation time implies a hi-viscosity solvent and
Now, lets just say I am studying the diffusion of methane in polyethylene.
To what extent will the damp affect the simulation. I mean to say is higher
the viscosity, lesser the diffusion, so to what extent the change in values
of damp affect the msd of methane. Moreover, can anyone tell me the range of
damp for polymers like polyethylene or is there a general way to decide.
that depends on how you are using fix langevin, i.e. as a weakly
coupled thermostat or to provide a (simple, if not crude) implicit
solvent model. which of the two it is, only you can know (from your
previous inquiries, i would suspected the former) and that determines
a meaningful choice of the damp factor.
as for impacting diffusion. yes, damping will affect diffusion. in the
case of a weakly coupled thermostat this can be crucial, but then
again, the use of fix langevin as a thermostat in these cases, is
merely to correct for excess energy generated by numerical errors of
the time integration, and your choice of MD parameters should be done
to minimize that (and thus the need for damping) in the first place.
in the case of an implicit solvent model, impacting the diffusion is
the whole purpose.
as for diffusion in a matrix, you obviously have not studied the
relevant literature on that topic and are approaching it in a very
naiive way. diffusing in a matrix is a tricky topic and requires good
understanding of the relevant statistical mechanics. it is also a well
studied field with lots of helpful and detailed papers on the subject
(not just polymer matrices, but also others like zeolithes and so on).
MD is often not the method of choice for these cases (especially under
ambient conditions) due to the limitations imposed by the high
barriers between various states.
I should apologize if I sound too clumsy but I couldn't find anything
relevant to my doubt on the internet.
actually, there should be plenty of information, but the problem is,
that you don't quite understand the issue, and that means, you need to
learn more about MD basics, which is best learned from text books and
discussing with and being tutored by experienced people (in person!).
in short, you are stongly recommended to do more background research
and receive tutoring on performing meaningful simulations on your
subject. this goes far beyond the scope of a mailing list (which make
for highly inefficient tutors).