Force Field for Molecular Dynamics Simulation of Dolomite Surface?

More Amir Hossein Saeedi Dehaghani's questions See All

GROMACS vs. LAMMPS in using GPU calculation capacity?

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....

09 October 2018 7,447 0 View

Why temperature does not maintain in molecular dynamics simulations under NVE ensemble?

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...

05 June 2018 9,553 0 View

Could anybody explain me how to obtain unknown potential parameters for a mineral crystal using GULP?

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...

03 April 2018 2,351 4 View

What's the physical interpretation for negative diffusion coefficient?

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...

03 April 2018 7,695 4 View

Cross term potentials for molecular dynamics simulation of Dolomite/Hydrocarbons?

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 4,900 2 View

Lj/cut/coul/cut vs. lj/cut/coul/long in LAMMPS?

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...

02 March 2018 6,218 3 View

How to select proper LJ mixing rule for several force field utilized simultaneously in a MD Simulation?

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...

02 March 2018 9,529 4 View

Please help me obtaining Mean Square Displacement (MSD) through molecular dynamics simulation?

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,...

02 March 2018 4,011 2 View

Is dihedral define for consecutive carbons in a benzene ring, i.e., C-C-C-C ?

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.

02 March 2018 9,147 3 View

Is there freely available HPC for running simulations?

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.

01 February 2018 1,941 4 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

How can we differentiate between calcite, dolomite, siderite, magnesite and ankerite minerals in carbonatite rocks in thin section under op microscop?

How can we differentiate between calcite, dolomite, siderite, magnesite and ankerite minerals in carbonatite rocks in thin section under optical microscope?

07 August 2024 2,132 3 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

Andrey Kyrylchuk

Some all-atom force field, like UFF, may be useful. But anyway you should look through recent papers in the field.

Qingwei Gao

Here is a paper may be useful to you.

Plastic deformation and twinning mechanisms in magnesian calcites: a non-equilibrium computer simulation study

Vladimir A. Basiuk

I would recommend a universal force field, like UFF (Gaussian) or MM+ (HyperChem), depending on the software package you use.