What does a negative potential energy (total energy) depict in a molecular dynamics simulation?

Hello to all,

I'm using REAXFF force field to build a PE model including bonds information. However, the system feedbacks with “ERROR on proc 0: Bond atoms 12 13 missing on proc 0 at step 10692 (src/ntopo_bond_all.cpp:60)”. Could anybody help with this? Thanks in advance.

Respected peers,

I am trying to simulate the lignin molecule with a mixture of ozone and water with reaxff potential (I used the reaxff potential available on the LAMMPS example.). I am getting some questionable values for pressure. While running for NVE simulation on the following system: lignin + 500 ozone + 3500 water for 1 ns and 0K starting temperature, the system recorded a very high negative pressure of negative tens of thousand. Later this value saturated to around -2000 as the simulation reaches the end of 1 ns (the temperature at the end of 1 ns is around 473 K). According to LAMMPS documentation, the pressure is supposed to be atm units (I used 'real' units). Considering the negative pressure, I incremented water molecules to 5000 but the pressure trend remained the same (I simulated this particular system for 10 ns). I am pretty new with LAMMPS and I will be grateful if someone will help me understand these results

Below is my input file and I am attaching my log file (for lignin + 500 ozone + 3500 water system).

units real

boundary p p p

atom_style charge

read_data data.lignin+ozone+water.charge

pair_style reaxff lmp_control

pair_coeff * * ffield.reax.cho C H O

group lig id 1:201

group ozn id 202:1701

group water id >= 1702

group lig+ozn id 1:1701

compute reax all pair reaxff

#compute pressure all pressure thermo_temp

variable eb equal c_reax[1]

variable ea equal c_reax[2]

variable elp equal c_reax[3]

variable emol equal c_reax[4]

variable ev equal c_reax[5]

variable epen equal c_reax[6]

variable ecoa equal c_reax[7]

variable ehb equal c_reax[8]

variable et equal c_reax[9]

variable eco equal c_reax[10]

variable ew equal c_reax[11]

variable ep equal c_reax[12]

variable efi equal c_reax[13]

variable eqeq equal c_reax[14]

thermo 1

neighbor 2.5 bin

neigh_modify every 10 delay 0 check yes

#velocity all create 300.0 4928459 mom yes rot yes dist gaussian

#fix 1 all nve temp 300.0 300.0 0.1

fix 1 all nve

fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff

fix 4 all reaxff/bonds 20 bonds.reaxff.lignin+ozone+water_nve300_1ns

fix 5 lig reaxff/bonds 20 bonds.reaxff.lignin+ozone+water(lignin)_nve300_1ns

fix 6 ozn reaxff/bonds 20 bonds.reaxff.lignin+ozone+water(ozone)_nve300_1ns

fix 7 lig+ozn reaxff/bonds 20 bonds.reaxff.lignin+ozone+water(lignin+ozone)_nve300_1ns

#fix 8 all press/berendsen iso 0.0 0.0 1000.0

#fix 5 all bond/break 5 1 1.9

minimize 1.0e-6 1.0e-9 10000 100000

log log.lignin+ozone+water.nve300_1ns

variable nqeq equal f_2

thermo_style custom step temp epair etotal press &

v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &

v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq

timestep 0.1

dump 1 all atom 20 dump.reaxff.lignin+ozone+water_nve300_1ns

dump 2 lig atom 20 dump.reaxff.lignin+ozone+water(lig)_nve300_1ns

dump 3 ozn atom 20 dump.reaxff.lignin+ozone+water(ozn)_nve300_1ns

dump 4 lig+ozn atom 20 dump.reaxff.lignin+ozone+water(lig+ozn)_nve300_1ns

restart 10000 restart.lignin+ozone+water_nve300_1ns

run 10000

Thank you in advance.

I use LAMMPS real units in a simulation of an adhesion test using Steered Molecular Dynamics (SMD).

The output of pulling forces using this fix thereby will be in kcal/mol-ang.

I would like to convert this to Newtons in SI units for post-processing but am struggling with the conversions.

From the conversions till now, I have been able to surmise this:

1 kJ/mol = 0.239006 kcal/mol = 1.66053 x 10^-11 J/m

1 kcal/mol = 1.66053/0.239006 x 10^-11 J/m = 6.9476 x 10^-11 J/m

So,

6.9476 x 10^-11 J/m = 6.9476 x 10^-11 N

Which means,

but this is in kcal/mol and not kcal/mol/ang ....am assuming there has to be a difference or is this calculation correct. It might be something really silly that am overlooking or getting wrong but I kindly request some help to verify this.

Any help is appreciated.

Hi, i'm a physics student working in a project of materials science. I'm doing a simulation using LAMMPS.

In this case, i have a problem with the error Lost atoms: original 60536 current 56624 (../thermo.cpp:427) once i run the script. I'm trying to put a graphene sheet in a fix nvt 10 kelvin. But once the fix it's running, in 4 steps the velocity becomes irrational and I get the error.

Can you please guide me please? I'm new in all this.

Thank you for the help.

I want to calculate the mass density profile of a pure organic solution over the course of an npt simulation in LAMMPS. Looking at the documentation there are a number of ways you can do this depending on how you carve up your system. My initial though was simply the mass of the molecules in the simulation (Nmolecules * (molar mass/ Avagadro's constant)) divided by the cell volume. However, if there is a choice in the way you carve up the system surely this will change the volume you are using?

The decision on how to 'chunk' your space can be done by specifying an atom type, a molecule or spatially (1D, 2D or 3D), presumably all these methods would give different volumes so affect the outcome. What would be the most reasonable way? 

additionally, how can we calculate different cooling rates when we melt a system up to 3300k and quench at room temperature for 10000000 steps

For more clarity on the question asked, here's what I want to do -

Model a polymer, stuff it inside a box and then shrink the box size to get required density.

The problem is, when I shrink it using 'Pstart' and 'Pstop' values in 'fix npt' as 1 1 or 1 0, the density of the system that 'thermo_style custom' command outputs is way below than the desired density.

To get over this, I gradually increase the pressure from 1 atm to 9869.23 atm (1GPa) and maintain it there. This brings me pretty close to the desired density for the system.

Now, I want to perform other production runs on the aforementioned system (the one close to desired density) but as soon as I perform npt fix which releases the pressure off the system i.e. equilibrating the system at 1 atm, the system volume shoots up thus drastically dropping down the density.

How do I maintain the density of the given system, independent of the external pressure applied or not on the system

Dear all,

I'm wondering if it is possible to use the molecular dynamics method to do some simulations about the electroplastic phenomenon to investigate the electric current effects on dislocation motions. I have not used molecular dynamics before, and I'm unsure if I can simulate the electric current charge in LAMMPS. So, if anyone could share references or ideas regarding this issue would be appreciated.

How do I do energy minimization in lammps with NVT ensemble ?

I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search line alpha. I am using the following command.

# initial minimization

fix 1 mobile nvt temp 315.00 315.00 100.0

min_style sd

minimize 1.0e-10 1.0e-10 200000 200000

write_data 100PU_water.minimized

unfix 1

What am I doing wrong ? If I use min_style as quickmin it runs for the entire duration but does not work in SD. Most importantly I need to do it in NVT. How do I do that ?

Thank you