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

More S. Xavier's questions See All

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

I am trying to obtain microstructure for Mg-Zn-Sn alloy?

Any suggestions with respect to etchant composition and holding time?

27 July 2024 6,925 2 View

How to get Scopus Author Index ??

18 July 2024 4,080 3 View

Dear researchers. pl help how to plot jablonski energy level graph and magnetic hysteresis curve in origin?

through origin software

17 July 2024 4,991 0 View

Do software tools exist to assess the economic and technical practicality of introducing new food products, such as yogurt with modified starch?

This question explores the world of food innovation and asks if there are computer programs that can analyze the financial and technical feasibility of introducing new food products. For instance,...

13 July 2024 7,446 0 View

My nanoparticle has a lower fluorescence life time of 2 ns (usual life time between 3-10 ns). what are the inferences I can get from this?

what all details we will get from fluorescence life time data

10 July 2024 505 1 View

Alternative binders other than Nafion solution?

Hi Everyone, I plan to deposit a catalyst (TS-1@Co-PDA, in the core: TS-1 zeolite with a shell of Polydopamine designed with Cobalt) on a rotating ring-disk electrode (RRDE) to evaluate the...

29 June 2024 8,203 3 View

Journal Report Impact Factor 2024?

Has the new journal impact factor for 2024 been released? pls send me updates if anyone has it.

19 June 2024 6,333 1 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

Gajanan Karunakaran

Hi Xavier,

What is the potential parameter you changed to rectify the issue LAMMPS WARNING: Bond/angle/dihedral extent > half of the periodic box length?

Thank you.