23 Questions 13 Answers 0 Followers
Questions related from Amir Hossein Saeedi Dehaghani
Dear all I'm a LAMMPS user, dealing with large-scale simulation, over 100,000 particles and >100 ns. Inevitably, I must utilize the GPU accelerating power to speed up my running performance....
10 October 2018 7,222 0 View
Dear researchers I have a fundamental question about essence of NVE ensemble. In that, we assume a constant number of particles are kept in fixed volume and their total energy is constant. This...
06 June 2018 9,472 0 View
Hi Researchers Does anybody know a paper reporting cross term potentials for molecular dynamics simulation of Dolomite/Hydrocarbons? My oleic system contains various kinds of heteroatoms such as...
04 April 2018 4,675 2 View
Hi everybody In my research career I want to obtain refit potential parameters, e.g., LJ or Buckingham, for a mineral structure. I've recognized a freely available software, namely, GULP, provide...
04 April 2018 2,130 4 View
Hi every researchers I'm working on ions transport in aqueous solution and aim to derive diffusion coefficient via slope of MSD (mean square displacement) vs. time. But, at the long time, MSD...
04 April 2018 7,584 4 View
Hi All I'm going to perform a MD simulation for a combination of hydrocarbons, ions, water and mineral. I realized that each FF has got its own LJ mixing rule, so, how should I select a mixing...
03 March 2018 9,310 4 View
Hi all researchers I'm going to perform a molecular dynamics simulation for benzene. I'm not sure if dihedral is defined for c-c-c-c in the ring. Does anybody have idea? Any hint is welcome.
03 March 2018 8,923 3 View
Dear All I'm new on LAMMPS and don't understand the physical and computational difference of handling long-range electrostatic interactions through lj/cut/coul/cut or lj/cut/coul/long. Any hint...
03 March 2018 5,985 3 View
Hi Everybody I'm new to concept of MD and want to use results of MD simulation to calculate MSD and accordingly diffusion coefficient of a kind of molecules. I'm going to write a code on my own,...
03 March 2018 3,791 2 View
Hi all I'm working on molecular dynamics simulation which requires great computational resources. Could anybody please let me know is there any free HPC for that purpose? Any hint is welcome.
02 February 2018 1,927 4 View
Hi everybody I'm familiar with protonation/de-porotonation process of metal oxides once changing pH. But, calcite is not such material. So, why does its surface charges alters by pH? Could...
02 February 2018 1,070 2 View
Hi all I've came cross many MD works where system charge was balanced (neutralized) through adding some arbitrary counter-ions. Why did they do that? What if simulating a charged system? Is it...
02 February 2018 2,353 5 View
Hi All Could anybody please introduce me some references for molecular dynamics simulation of dolomite? I'm seeking for a force field. Any hint will be appreciated.
02 February 2018 9,772 3 View
Hi Everybody I'm going to carry out MD simulation using LAMMPS in order to get IFT of two neighboring fluids. Firstly, what's the best ensemble? and what should I do? I've recently realized the...
02 February 2018 3,870 4 View
Hi everybody Does anybody know how obtaining free licence of ATK-VNL software? I need this tool for MD simulation. Thanks in advance
02 February 2018 4,870 6 View
I'm new to subject of Force field. I'd like to know how FF, particularly those for proteins, are derived? Through experiment or QM calculations? How parameters were optimized? Is there any...
02 February 2018 7,993 3 View
I'd like to run a molecular dynamics simulation to simulate aggregation of asphaltene molecules in heptane/toluene. Does anybody know what's the proper force field to do so? As I know, common FF...
01 January 2018 4,347 2 View
Throughout an extensive literature survey I realized that there is a difference in modelling asphaltene precipitation phenomena and using different EOS. Am I right?
01 January 2018 9,434 4 View
Dear All, I am trying to simulate a box of water having density 1gm/cm3 and 10,000 molecules using LAMMPS. The issue which I am facing is that I am not able to maintain the pressure constant. It...
01 January 2018 1,868 2 View
I'm new in concept of PMF. Could anybody please let me know how to obtain it through LAMMPS. Please explain the physical concept of this quantity and it derivation through MD. Bests
01 January 2018 7,936 4 View
I'm aware of taking a minimum size of simulation box to be greater than cut-off distance. However, does taking an excessive large box affects on MD simulation? Sincerely
01 January 2018 9,504 4 View
Is it possible to obtain entropy of a system through MD simulation? If yes, what's the underlying formulation? If not, why?
01 January 2018 2,064 5 View
I'm new to MD simulation and could not understand how different termstat and barostat works. Could anybody please introduce me an illustrative references? Thanks so much in advances.
01 January 2018 4,497 3 View
