Any suggests about LAMMPS Error:"ERROR on proc 0: Bond atoms % % missing on proc 0 at step % (src/ntopo_bond_all.cpp:60)"?

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 am trying to run a longer simulation with SPCE water model provided within the lammps benchmark files. I get the error: Out of range atoms - cannot compute PPPM, after I set the timestep for 1fs.

I need a longer time frame for my Structure Dynamic Factor calculation. ANy help would be appreciated.

Dear all

I'm using LAMMPS to simulate the lipid bilayer from CHARMM-GUI Membrane Builder.

After the MD simulation I want to convert LAMMPS dump file to pdb file. Is there any tool or software that makes it easy to convert? If it is possible, please guide me the following way.

Thank in advance.

I am trying to run nemd shock simulation on water through momentum mirror technique with tip4p flexible potential. Errors originated due to change of periodic boundary to fixed condition along shock propagation direction (here along Z). First error was tip4p hydrogen missing which I sorted out with help of pbc wrap command in VMD as suggested by Axel Sir. The molecules with fragments on other side were identified and slightly shifted in order to occupy completely inside box. This does not affect the density or initial temp. of 300K. Next error was regarding the use of kspace style pppm/tip4p which is only applicable for periodic boundary conditions. This was sorted with help of kspace_modify slab command applicable for p p f boundary condition. Further errors were Angle atoms 2576 2577 2578 missing on proc 19. I was introducing a gap of 2 nm between molecules and walls of reflection in order to prevent from unsteady shock. As the gap was removed, angle atoms missing error was sorted out. I don’t know the reason behind it. It was just a trial result. Now I am facing same type of error of “bond missing atoms on proc 0 at step 65” along with “out of range atoms-cannot compute pppm”. I tried with different timestep but result is same. Also this can’t be due to multiprocessor simulation as I had tried it with 1 cpu also. I had followed many Lammps threads regarding above mentioned errors.

I am working on hydroxyapatite crystal. The structure is available in .cif , .pdb formats.

I want to convert it into a LAMMPS input file with all angles and bonds.

Can anybody help me in this? 

Hello!

I am currently doing an MD simulation with LAMMPS and calculating the interaction energy between two groups. However, the group/group command only gives the total interaction energy, including Van der Waals and electrostatic interaction energy. I am wondering, is there any method to dump them separately?

Thank you in advance!

Dear Lammps users, I am experimenting with a toy system constituted by 1024 water molecules (tip3p) confined in a

-25 25 xlo xhi

-30 30 ylo yhi

-30 30 zlo zhi

box and (for the moment) 1 p-phenylene diamine molecule in a

35 45 xlo xhi

-10 10 ylo yhi

-10 10 zlo zhi

box

Both systems were equilibrated with 300 ps NVT at 300 °K

I combined the two systems in one to test its proper functionality.

I got this message:

ERROR: Dihedrals defined but no dihedral types (src/read_data.cpp:1198)

Last command: read_data dat-PPDA-1-00 add append

I attach the input file and the PPDA data file

Any cvomment or diagnosis will be really welcome

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

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?