LAMMPS WARNING: Bond/angle/dihedral extent > half of periodic box length. How to rectify it?

More S. Xavier's questions See All

What are the steps to calculate bond dissociation enthalpy in gaussian?

For example, in phenol, how to calculate the bond dissociation enthalpy of each bond using gaussian? What are steps?

08 September 2019 5,174 3 View

Why the theoretical values (vibrational and NMR ) obtained through Gaussian is greater than experimental values?

Why the theoretical values (vibrational and NMR ) obtained through Gaussian is higher than experimental values? NMR was computed using GIAO technique and vibrations were calculated using B3LYP...

05 June 2019 8,671 5 View

What are the books/papers to learn about quantum confinement in 1D, 2D and 0D nanostructures?

What are the books/papers to learn about quantum confinement in 1D, 2D and 0D nanostructures? What are books/papers to know more about nanoelectronic devices?

31 December 2018 1,540 8 View

How to proceed with molecular dynamic simulations in nanoscale?

How to commence simulations in nanoscale? In which part of the code do we introduce the nano dimensions?

11 December 2018 6,285 7 View

How to calculate thermal and electrical conductivity of an organic compound using Molecular dynamic simulations?

10 November 2018 842 4 View

How to view the conformational change in the protein after MD simulations of protein ligand complex?

How to view the conformation change in protein after 50 ns MD simulations?

01 February 2018 9,503 3 View

In gaussian calculation, what does negative polarizability of an isolated molecule indicate?

In Non-linear optical activity what does negative polarizability of an isolated molecule indicate (through gaussian calculation)?

10 November 2017 5,004 1 View

How to make a Journal indexed in Scopus?

We have multidisciplinary Journal in the college (St. Joseph's Journal of Humanities and science). We publish Research articles in all the disciplines. Till now we have published 8 issues as four...

09 October 2017 3,422 5 View

What is meant by pi-alkyl, pi-pi T shaped and pi-Sulphur interaction in protein-ligand binding?

Can anyone suggest books/papers which clearly explains pi-alkyl, pi-pi T shaped and pi-Sulphur interaction?

09 October 2017 2,583 4 View

How to fix the following mpirun error?

I do MD simulations in SGE cluster using gromacs 5.0.2 version. After exporting the path and libraries correctly, I gave the following commands gmx grompp -f mdp/eql2.mdp -o eql2 -pp eql2 -po...

08 September 2017 9,522 3 View

1. If I can quantize the atom using this hyperbolic spiral and classical physics, could nature do the same?

If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...

07 August 2024 5,343 2 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 2 View

Why reactivity isn't increased with more empty spots in valence shell?

If from a geometric perspective the non-halogens, non-noble gases have more empty spots in their valence shell, and the filling/exiting of any of the empty spots in the shell constitutes a...

03 August 2024 4,787 2 View

Why do paired electrons atoms produce no magnetic field lines?

If you think of electrons with spin as bar magnets, you know bar magnets of opposite polarity as long as they're not occupying the same spatial location don't cancel out each other's magnetic...

03 August 2024 3,927 2 View

Does continues partial charging/discharging do any harm to the BESS performance and degradation?

For a grid connected BESS (lets say 100 MW/200 MWh system, LFP battery), if we charge the BESS in such a way that whenever we can access power from the solar that will charge the BESS. Hence it...

01 August 2024 9,903 7 View

How to Post-fix Mice pup's brains?

I need to Postfix mice brains. I slice the brains using microtome at 40 microns. These are Postnatal days 7, 11, 14, and 21. I am using half the brain for other analysis, so I need to fresh freeze...

31 July 2024 1,123 4 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

30 July 2024 1,607 1 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

James McDonagh

Hi, I have never used LAMMPS specifically, but it sounds like your box is too small. Can you not just increase your simulation box?

What molecule are you trying to simulate and how big is your box already? Is the system solvated or in vacuum?

Ramin Ekhteiari Salmas

How do you define or construct the system box? It seems that, there is a main periodic problem in the system.

S. Xavier

Have rectified the error. Changed a potential parameter. It works well