13 Questions 67 Answers 0 Followers
Questions related from Sayyed Jalil Mahdizadeh
Hi, Imagine that you are going to sample a protein conformation (consists of N atoms) using Monte Carlo and Molecular Dynamics simulations, independently. For the MD simulation, the phase space...
07 December 2022 346 6 View
Hi all, What is the best way to draw a FES diagram for a metadynamics simulation with 3 CVs? I know that it is still possible to draw 2D FES diagram with two CVs and project the Free energy...
12 December 2021 935 4 View
Hi all, What is the best free software/code to calculate free energy Perturbation (FEP) analysis on receptor-ligand complex?
15 October 2020 3,338 5 View
The delivery hydrogen uptake was specified to the difference between H2 uptake at charging pressure (say 100 bar) and discharging pressure (say 5 bar) both at the same temperature (e.g. 77 K). But...
06 October 2018 4,629 3 View
Dear colleagues, I'm beginner in C++ programming, I've coded a c++ program to solvate (hydrate) a structure (carbon nanotube for instance). Would you please check it out and give me your comments...
04 February 2017 7,359 9 View
Dear C++ experts, I'm a beginner with C++ and I've programmed my first numerical game for training. Here, a random number was chosen between 1-15 and the gamer has three chances to guess the right...
08 January 2017 8,065 10 View
Dear LAMMPS users I was going to run a MD simulation with about 24000 atoms on 8 threads parallel calculations, but I get the following error after 450 cycles: Process 3 exited without calling...
21 November 2016 7,674 3 View
LAMMPS computes the total energy of a single graphene sheet with 1000 atoms in kcal/mol unit. Does it make any sense?
08 December 2015 514 5 View
Dear all Could all atoms zero partial atomic charge be an option for charge equilibration (QEq) method as implemented in LAMMPS? http://lammps.sandia.gov/doc/fix_qeq_reax.html
04 November 2015 7,573 4 View
What are the simulation conditions to perform a MD simulation in nano-scale e. g. graphene nanoribbons or semiconductor nano-particles. I mean what would be the simulation box domain? Should the...
08 October 2014 1,188 3 View
Which potential is the best choice for considering the interaction between copper nanoparticles dispersed in water and which one is the best for interaction between water-copper nanoparticles?
20 January 2014 4,889 4 View
As you know, electronic contribution to thermal conductivity for metals is as significant as (or more significant than) phonon contribution (K=Ke+Kph). My question is: do electrons contribute to...
16 January 2014 561 5 View
I'm going to perform an explosion simulation. Any advice or suggested software?
16 December 2013 4,393 10 View
