simulations
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?
How do you define or construct the system box? It seems that, there is a main periodic problem in the system.
Have rectified the error. Changed a potential parameter. It works well
For example, in phenol, how to calculate the bond dissociation enthalpy of each bond using gaussian? What are steps?
08 September 2019 4,731 3 View
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 8,487 5 View
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 1,370 8 View
How to commence simulations in nanoscale? In which part of the code do we introduce the nano dimensions?
11 December 2018 6,127 7 View
How to calculate thermal and electrical conductivity of an organic compound using Molecular dynamic simulations?
10 November 2018 671 4 View
How to view the conformation change in protein after 50 ns MD simulations?
01 February 2018 9,363 3 View
In Non-linear optical activity what does negative polarizability of an isolated molecule indicate (through gaussian calculation)?
10 November 2017 4,793 1 View
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 3,274 5 View
Can anyone suggest books/papers which clearly explains pi-alkyl, pi-pi T shaped and pi-Sulphur interaction?
09 October 2017 2,225 4 View
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 9,335 3 View
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
(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
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
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
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
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
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
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 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
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