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Re: [lammps-users] Reg: Interaction energy calculation between two molecules in a system
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Re: [lammps-users] Reg: Interaction energy calculation between two molecules in a system

From: Ray Shan <rshan@...1795...>
Date: Tue, 22 Aug 2017 20:04:33 +0000

It is perfectly reasonable – why do you think there is something wrong?


On 8/22/17, 12:19 PM, "ZEESHAN AHMED" <pg201271008@...6800...> wrote:

Dear all,

I have built a system with fix boundary conditions containing two rigid gas molecules at different geometries to calculate the total energy of the system and also the interaction energy between the molecules.  I didn't do any minimization and didn't consider bond energy angular energy etc. as I am just interested in calculating the energy of rigid molecules at various distances. When I varied the distance from 2 Angstrom to 6 Angstrom without doing any optimization to calculate the energies, the values vary from 1496 kcal/mol at 2.5 Angstrom to -1.9 kcal/mol at 6 Angstrom. I have used fix rigid/nve keeping force and torque flags equal to zero to simply calculate the energy of the two molecule system. Please see the code attached. Did I do any thing wrong in the code?

units       real
atom_style full

# setup problem
dimension 3
boundary    f f f
read_data      data.gas_dimer
pair_style lj/cut 12
pair_coeff      1 1 1.5890  2.785
pair_coeff      1 2 2.6892  2.8995
pair_coeff      2 2 4.5512  3.014

#group A molecule <> 1 3
#group B molecule <> 4 6

#fix 1 all nve
#fix 2 A setforce 0.0 0.0 0.0
#fix 4 B setforce 0.0 0.0 0.0

fix         NVE all rigid/nve molecule force 1*2 off off off torque 1*2 off off off

thermo_style custom step etotal epair temp vol press density

timestep     1

run           10000
Thanks and Regards
Zeeshan Ahmed