There is a lot of literature on self-assembly of lipid bilayers or vesicles, particularly
in coarse-grained models where it will happen much more quickly
and thus cheaply (in a computational sense). This is driven by choosing
LJ params for the different particles that induce hydrophobic or phyllic
effects with respect to solvent particles. I imagine you could do something
similar with a free surface. Step (4) is simply changing the simulation box shape
over time, see the fix deform command.
Hi steve, thanks for having answered to my message. Actually I hoped to find in the list somebody working on the same or very similar subject, so to exchange experiences, suggestions and maybe errors and solutions. Actually there is plenty of literature available, the largest share of it being related to lipid bilayers, as you stated. I found very little on my specific topic (modeling of on-surface synthesis of 2-D polymers): too bad.
I would not like to use coarse grained model because I need to “see” the actual (complex) molecules conformational behavior and the possible emergence of a regular disposition. I am ready to pay the computational price…, up to a certain level of course.
I will test the fix deform command. A question for you, if I may: I am puzzled about which remap keyword I should use in order to make the simulation as close as possible to the physical merchanism: actually, when the barrier is moving the molecules closer to the barrier are pushed forward, they in turn push other molecules closer to them and so forth. Before receiving your message I was thinking to use fix wall harmonic. Any comment will be really welcome.
I understand that very likely I am moving outside the scope of the Users mailing list, so please accept my apologies
The fix deform doc page has advice about the remap keyword. If you’re not sure,
I suggest you try a couple options and monitor the simulations to see what you think.