LJ/CUT potential

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1

Daer All users

I need to use lennard jones potential for my model but i'm already
confused with global Cut-off parameter. in my model i have Oxygen,
Calcium ,phosphor , Hydrogen which are unbounded so when I set this
potential for my simulation model I should set epsilon and sigma in
pair_coeff command. I dont' know the role of global cut-off. When i
chose uper than 1 some atoms missed. here is my code:

pair_style lj/cut ???
pair_coeff 1 1 0.001229498 2.941736 #CAL-CAL
pair_coeff 1 2 1.85725E-05 2.986590077 #cal-O
pair_coeff 1 3 3.65136E-05 3.201945521 #CAL-P
pair_coeff 1 4 1.22815E-05 2.016228794 #CAL-H
pair_coeff 1 5 1.26564E-05 3.016160792 #CAL-O(H)

pair_coeff 2 2 0.002611857 3.032545038 #0-0
#pair_coeff 2 3 0.005134916 3.251214178 #O-P
pair_coeff 2 4 1.79003E-05 2.047252709 #O-H
pair_coeff 2 5 0.001779873 3.062570761 # O-O(H)

pair_coeff 3 3 0.010095256 3.485650996 # P-P
pair_coeff 3 4 3.5192E-05 2.194874915 #P-H
pair_coeff 3 5 0.003499235 3.28340498 #P-O(H)

pair_coeff 4 4 1.22679E-07 1.382087851 # H-H
#pair_coeff 4 5 0.010095256 3.485650996 #H-O(H)

pair_coeff 5 5 0.001212911 3.092893773 # O(H)-O(H)

2

Daer All users

I need to use lennard jones potential for my model but i'm already
confused with global Cut-off parameter. in my model i have Oxygen,
Calcium ,phosphor , Hydrogen which are unbounded so when I set this
potential for my simulation model I should set epsilon and sigma in

...and you can represent this with a simple lj/cut
potential *without* any (partial) charges???

pair_coeff command. I dont' know the role of global cut-off.

what exactly is your question?

are you confused about how the cutoff is chose
or what a cutoff is at all?

the documentation page explains is very clearly
how the cutoff is applied and what the global vs.
the per pair cutoff logic is.

When i
chose uper than 1 some atoms missed. here is my code:

losing atoms usually means, that you simulation
is going down the drain due to incorrect input, be
it a bad choice of parameters or a bad choice of
an initial geometry.

axel.