How to calculate the acceleration/velocity of different molecules in an MD Simulation?

Hi, If I am performing an MD Simulation in which the two groups/molecules are moving in a direction on applying a force on the system, how would I calculate the velocities/acceleration of the two?...

08 February 2021 9,525 4 View

Student writing his own Learning Outcomes - is this the way forward?

'Students just dont want to study; they are here to waste time!' I have heard this phrase many times; so are the students solely to be blamed? We will find many students who just dont seem to...

04 February 2021 8,546 22 View

What if we go for one single global currency?

What if we go for one single global currency? than every country has its own currency. Currency exchange commission etc. (Advantages/Disadvantages)

04 February 2021 8,937 3 View

Conflict resolution at socio-economic disparities?

Conflict resolution at socio-economic disparities? Two-way honest approach driving through varying characterized bi-parental upbringing, that further leads societal interactions into one to one,...

14 January 2021 7,589 1 View

Socioeconomic loss vs gain?

Considering the majority of the population, as if, they do not know as to what is their strength. This perhaps is due to their considerably lesser exposure to various possibilities, as a result...

14 January 2021 8,720 2 View

Data misrepresentation and Ignorance of socio-economic factors?

Do you think the majority of developing, underdeveloped, and even the developed countries lack in capturing the finer elements of behavioral data generated at various interactive and reactive...

13 January 2021 3,241 2 View

Is recycling a challenge to the governments of developing countries?

Is recycling a challenge to the governments of developing countries? A strong will for more serious aggressively organized recycling initiatives, embedded with strict regulations supported through...

12 January 2021 510 13 View

Variant or strain, what exactly happened to the corona virus ?

The new, more contagious variant of the virus that causes COVID-19 which initially detected in the U.K. and has now been spotted in many of the country. While some have referred to this as a new...

11 January 2021 8,810 5 View

The hospitals reported rise in ICU admissions of young COVID patients - Is the new strain of COVID to be blamed?

05 January 2021 3,141 12 View

What are those FACTORS that strongly suggest that the same workers come from India to GCC have played noticeable role, but why not in India?

Research is needed to identify the factors responsible for not so well utilized workforce for the development in India when the same workforce have played a role to obtain strikingly visible...

04 January 2021 8,548 2 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View