Hi everyone!

I have a few questions about my dynamics.

My system consist of a biomolecule (generated by charmm2lammps tool) plus a silver cluster, solvated in water. I treated silver atoms with EAM, the biomolecule by lj/charmm/coul/long and between those a lj/cut, by hybrid/overlay pair style. For that, i’ve generated the solvated biomolecule data file by charmm2lammps and added manually the silver atoms positions. Because i assigned the EAM potential to silver atoms in my data file, i’ve put the lj/cut interaction in the input file, is there a better way to do it?

The thing is, when i run de dynamics, i get a warning: “WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (…/pair.cpp:211)”. Is

that because i’ve assigned EAM to silver atom and then i tell LAMMPS to compute a two-body interaction with the biomolecule?

And other question is, in the case i want to put some charge state to my metal cluster (let’s assume the charge redistribute equally upon the atoms in the cluster), +5 for example, it is okey to asigne a simple EAM+coul interaction between silver atoms?

In general, the dynamic is okey? Waht should i check to see if i can trust the result?

Here is part of my input and data files:

----------------------------------------- INPUT --------------------------------------------------

# Created by charmm2lammps v1.8.1 on jue may 21 18:06:18 ART 2015

processors 2 2 2 # nx*ny*nz = N procesadores

units real

boundary p p p

neigh_modify delay 0 every 1 check yes

pair_style hybrid/overlay eam lj/charmm/coul/long 8.0 10.0 coul/long 10.0

atom_style full

bond_style harmonic

angle_style charmm

dihedral_style charmm

improper_style harmonic

read_data Green1_wb_ions.data

# type 39 - Ag+

# type 40 - Ag0 (o con alguna carga)

pair_coeff 40 40 eam Ag_u3.eam # eam Ag-Ag

pair_coeff 40 40 coul/long # coul Ag-Ag

pair_coeff 1 40 lj/charmm/coul/long 0.445729 1.50001

pair_coeff 2 40 lj/charmm/coul/long 0.810506 2.87529

pair_coeff 3 40 lj/charmm/coul/long 0.445729 1.50001

pair_coeff 4 40 lj/charmm/coul/long 0.445729 1.50001

pair_coeff 5 40 lj/charmm/coul/long 0.445729 2.27999

pair_coeff 6 40 lj/charmm/coul/long 0.445729 1.50001

pair_coeff 7 40 lj/charmm/coul/long 0.30825 2.47599

pair_coeff 8 40 lj/charmm/coul/long 0.347753 2.4938

pair_coeff 9 40 lj/charmm/coul/long 0.321957 2.4938

pair_coeff 10 40 lj/charmm/coul/long 0.657191 2.99271

pair_coeff 11 40 lj/charmm/coul/long 0.657191 2.99271

pair_coeff 12 40 lj/charmm/coul/long 0.657191 2.99271

pair_coeff 13 40 lj/charmm/coul/long 0.623466 2.99271

pair_coeff 14 40 lj/charmm/coul/long 0.623466 2.99271

pair_coeff 15 40 lj/charmm/coul/long 0.569144 2.99271

pair_coeff 16 40 lj/charmm/coul/long 0.569144 2.99271

pair_coeff 17 40 lj/charmm/coul/long 0.569144 2.99271

pair_coeff 18 40 lj/charmm/coul/long 0.293905 3.32679

pair_coeff 19 40 lj/charmm/coul/long 0.293905 3.32679

pair_coeff 20 40 lj/charmm/coul/long 0.491797 3.09071

pair_coeff 21 40 lj/charmm/coul/long 0.491797 3.09071

pair_coeff 22 40 lj/charmm/coul/long 0.580415 3.11743

pair_coeff 23 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 24 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 25 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 26 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 27 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 28 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 29 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 30 40 lj/charmm/coul/long 0.929408 2.94816

pair_coeff 31 40 lj/charmm/coul/long 0.719917 2.81453

pair_coeff 32 40 lj/charmm/coul/long 0.719917 2.81453

pair_coeff 33 40 lj/charmm/coul/long 0.810506 2.87689

pair_coeff 34 40 lj/charmm/coul/long 0.719917 2.81453

pair_coeff 35 40 lj/charmm/coul/long 0.810506 2.87689

pair_coeff 36 40 lj/charmm/coul/long 0.810506 2.87689

pair_coeff 37 40 lj/charmm/coul/long 1.58953 3.21543

pair_coeff 38 40 lj/charmm/coul/long 0.450068 2.51496

pair_coeff 39 40 lj/charmm/coul/long 0.000000 0.00000