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 7,198 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 9,432 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 2,107 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 7,557 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 4,646 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 5,850 3 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 3,766 2 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 9,288 4 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 8,903 3 View

Must system charge be neutral for performing molecular dynamics simulation?

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...

01 February 2018 2,331 5 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 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.