Dear EMC,
I have been trying to reproduce the interphase Monte Carlo simulations (P.J. in ’t Veld et. al. Macromolecules 2006, 39, 439) for a system of linear PE chains using EMC. I have constructed the initial PE crystalline structure and defined the crystalline and interphase regions. However, when I tried to apply MC moves, it seems that only displace and rebridge moves were accepted. The output file shows the accepted and total trials for rotate, endbridge, and reptate are zero:
displace → {active → true, frequency → 1, dlimit → 10.02261058, nsites
→ 1, couple → true, n → 2, dmax → {0.505187504265, 0.505187504265},
accept → {{15531752, 7790121}, {0, 0}}},
endbridge → {active → true, frequency → 1, nmin → 3, nmax → 0,
tolerance → 0, dmin → 0, dmax → 5.58108093844, n → 1, accept → {total
→ 0, accepted → 0}},
migrate → {active → true, frequency → 0, target → ch2, radius → 0, n →
1, accept → {total → 0, accepted → 0}},
rebridge → {active → true, frequency → 1, drivers → 0, tolerance → 0, n
→ 1, accept → {total → 13498582, accepted → 7599756}},
reptate → {active → true, frequency → 1, nmin → 3, n → 1, accept → {
total → 0, accepted → 0}},
rotate → {active → true, frequency → 1, nmax → 3, n → 1, amax →
0.785398163397, accept → {total → 0, accepted → 0}}.
I noticed that each move has different input parameters. However, I was not able to find the definitions of these parameters in the manual. Could you please kindly help me understand how all these moves can be applied to the system? Thank you very much!
Please find below my EMC script:
(* EMC: Script *)
variables = {
output → “PE_MC”
};
get = {name → “PE_initial_structure.emc”};
(* define simulation properties *)
simulation = {
output → {debug → false},
systems → {properties → {t → 10000}},
types → {
skin → 0.6,
neighbor → pair,
virial → false,
stencil → standard,
standard → {correct → {active → false}}},
moves → {ncycles → 3648, seed → 123456789,
displace → {frequency → 1},
rotate → {frequency → 1},
endbridge → {frequency → 1},
reptate → {frequency → 1},
rebridge → {frequency → 1}},
blocks → {frequency → 100},
profiles → {frequency → 10}
};
flag = {flag → {fixed},
region → {shape → cuboid, type → relative, center → {0, 0, 0.-0.45},
radius → {2, 2, 0.05}}};
flag = {flag → {fixed},
region → {shape → cuboid, type → relative, center → {0, 0, 0.45},
radius → {2, 2, 0.05}}};
(* calculate initial energies *)
force = {style → init, message → true};
run = {ncycles → 20000, nblocks → 100};
memory = {style → full};
(* display resulting energy and recalculate final energies in several ways *)
force = {style → none, message → true};
force = {style → list, message → true};
force = {style → init, message → true};
(* output results to several output formats *)
put = {name → output};
pdb = {name → output, system → 0, cut → true,
forcefield → standard};
lammps = {name → output, system → 0, mode → put,
units → lj, types → true, forcefield → standard};