What is the Y-axis depicted exactly during calculation of RMSD distribution using "g_cluster" of Gromacs Package?

16 April 2015 1 6K Report

During calculation of RMSD distribution using "g_cluster", the Y axis of the XVG file denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it exactly is as well as how the calculation happened.

Aritra Bej

Do you get RMSD distribution from g_rms?

Badges
Science topic

More Aritra Bej's questions See All

Do anyone has soft copy of "Mathematics for biological scientists by Aitken"?

Its a book related to biostatistics.

27 April 2020 6,371 2 View

How to reduce the resistance of the battery or a capacitor?

I am doing a project on super capacitor. there is no equipment or technology to capture the electrical energy in a strike or in a fraction of second. but if we reduce the resistance of the battery...

20 March 2020 1,542 1 View

Help to add a new field equation in COMSOL ?

I want to solve an extra field along with the structural mechanics module in COMSOL. Basically, I want to use the stress which you obtain by solving a linear elastic problem, calculate the...

24 January 2019 8,669 1 View

What is the best tool to identify and provide a good pictorial representation of homologous DNA sequences between species?

I want to identify homologous DNA sequences between mouse chicken, xenopus and zebrafish for a human non coding genomic regions. Any suggestion of which tool to use. I would prefer the one that...

03 April 2018 2,394 3 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