I want to simulate a coarse grained molecule attached to an fcc 111 LJ surface. The steps that I took are as follows:
Created a LJ substrate (parameters corresponding to gold) with a LJ 93 wall on one end of the z direction and periodic boundary conditions on the x and y direction. The z direction had shrink wrap boundary.This substrate was then heated to high temperature (NVT) then cooled in steps to room temperature (300K).
The coarse grained molecule has two beads bonded together carrying a tabulated potential. I laid this molecule out on the free 111 surface and connected it to one of the surface particles through a bond governed by a morse potential. I did this by just taking the coordinates of the particles from the previous simulation. An LJ 93 wall is set up on the other end along the z direction of the substrate. Also I use the same boundary conditions as in the previous scenario (x ,y periodic, z shrink wrap).
Now when I turn on NVT fix at 300K the bond that I use to attach these molecules is stretched quite far implying that the molecules are not attached to the substrate. The bond energy is significantly higher than the energy kbT and I am not able to understand why this happens.
I would appreciate any pointers towards this simulation?
I want to simulate a coarse grained molecule attached to an fcc 111 LJ
surface. The steps that I took are as follows:
1. Created a LJ substrate (parameters corresponding to gold) with a LJ 93
wall on one end of the z direction and periodic boundary conditions on the x
and y direction. The z direction had shrink wrap boundary.This substrate was
then heated to high temperature (NVT) then cooled in steps to room
temperature (300K).
2. The coarse grained molecule has two beads bonded together carrying a
tabulated potential. I laid this molecule out on the free 111 surface and
connected it to one of the surface particles through a bond governed by a
morse potential. I did this by just taking the coordinates of the particles
from the previous simulation. An LJ 93 wall is set up on the other end along
the z direction of the substrate. Also I use the same boundary conditions as
in the previous scenario (x ,y periodic, z shrink wrap).
Now when I turn on NVT fix at 300K the bond that I use to attach these
molecules is stretched quite far implying that the molecules are not
attached to the substrate. The bond energy is significantly higher than the
energy kbT and I am not able to understand why this happens.
sorry, but my crystal ball is still in repair. nobody can say anything
for certain from such a vague description. can be anything: incorrect
visualization, bad initial configuration, bad parameters, bad
simulation protocol. you best chance is to talk in person with
somebody local that knows how to run MD.
Maybe you just placed your molecule a bit too deep into the repulsive side of the potential. Try running a minimization prior to switching on the thermostat. But like Axel said, guessing like this is a mad game.
Carlos