15 Questions 8 Answers 0 Followers
Questions related from Amir Hossein Saeedi Dehaghani
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...
08 April 2018 10,039 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...
05 April 2018 8,511 4 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...
03 April 2018 4,571 2 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.
22 March 2018 2,864 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,...
18 March 2018 4,716 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.
20 February 2018 8,796 3 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 8,438 2 View
Hi everybody Does anybody know how obtaining free licence of ATK-VNL software? I need this tool for MD simulation. Thanks in advance
01 February 2018 6,834 10 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...
01 February 2018 2,122 3 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.
31 January 2018 4,818 3 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
26 January 2018 4,785 6 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
24 January 2018 9,732 3 View
Could anybody let me know the chemical and physical difference between asphaltene and resin, such as molecular weight, H/C ratio, number of aromatic rings, length of aliphatic chains and so forth....
24 January 2018 3,830 6 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...
18 January 2018 2,895 2 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...
18 January 2018 1,695 2 View
