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

More S. Xavier's questions See All

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 3 View

What information can be had from raman at higher wavenumber?

i have recorded raman spectra of strontium oxide thin film. the spectra were recorded in the range 400 to 4000 cm-1. i have reference to peaks upto 1000cm-1. but i couldn't find literature for...

26 February 2021 2,499 1 View

What are the methods used for CNT..?

Respected Professor's i hope you are doing well and happy. i need some information about carbon Nanotubes. before blending the CNT with the matrix the CNT has been introducing in some treatments....

24 February 2021 5,383 5 View

Langevin Dynamics in shear flow?

Hi, We are trying to simulate particles with Langevin dynamics in a shear flow by Lees-Edwards boundary conditions in MD simulations. It seems thermal forces and shear flow do not go hand in...

23 February 2021 1,761 1 View

How we can measure Kemp % in wool without using of benzene?

Would you please let me to know about the methods for measurement of medullation and Kemp % on animal? My problem is that the wool sampling and sending to laboratory is not possible. So I would...

21 February 2021 7,260 4 View

Which is the best software or programming language (user friendly) for analysing data?

I have a basic knowledge on Python, R and MATLAB in analysing data. Among those, which is the best and user friendly? Which one should I learn deeply to analyse data?N:B: I want to learn data...

20 February 2021 3,950 15 View

Hi..how to isolate crude HDL (all subfractions) from human serum by size exclusion chromatography?

I would like to know about isolation of crude HDL from serum by SEC. Is it possible to perform with a serum sample volume of

19 February 2021 5,576 2 View

What is the reason film thickness increased?

what is the reason film thickness increased when increased doping concentrations give some reasons The measured film thickness is 156, 282, 394, 548 and 681 nm for 0, 1.5, 2.5, 3.5, and 4.5 wt....

17 February 2021 8,987 5 View

Do you have any experience with transfection of EBV immortalized B cells with Lipofectamine?

I know that efficiency of transfection for primary B cells is very low with Lipofectamine. But I did not try that for EBV immortalized B cells. Do you have any experience with transfection of EBV...

05 February 2021 4,159 1 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Energy minimization in LAMMPS using NVT ?

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...

01 March 2021 2,294 3 View

How can I edit suggested publications?

Hi there! I regularly receive suggestion about papers and authors that are totally out of my area. Does anybody know how I can fix this? Thank you!

01 March 2021 9,574 4 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

Can you perform the Murexide test on samples fixed in Formalin?

I have a fixed sample and would like to use the murexide reaction to test for uric acid composition. I no longer have fresh samples

22 February 2021 1,328 1 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Monte Carlo simulation?

Hi, i am conducting a Monte Carlo simulation for my new distribution but the MSE values are increasing while the sample size increase, does any experience this issue before and what should i do...

22 February 2021 3,680 4 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

How would I use a glycerol fixation to fix whole brain Drosophila tissue?

I need to take IF images with DAPI on a confocal but I need to use a glycerol fixation. Has anyone done this method before, if so how was it done? Thank you.

21 February 2021 3,081 3 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.