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

Why should we choose deep learning to machine learning? Why is CNN better for image classification? Can I get Typical Answer?

What Characteristics makes CNN work better?

03 March 2021 1,458 4 View

What are some of the research gaps in machine learning and artificial intelligence in africa?

i would to know some of the research gaps in the artificial intelligence field in most african countries.

03 March 2021 6,145 3 View

Anyone plz suggest relevant topic for research in image processing+Deep learning.?

I have selected brain tumor images ...but now found that already lots of research done n this topic.

03 March 2021 5,774 3 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 View

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02 March 2021 3,060 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