How would I do MM-PBSA analysis after MD simulations in GROMACS?

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I need a proper step by step tutorial for proper forest plot formation in metaanalysis of biological data. Can anyone help me?

In metaanalysis or systematic review, forest plots are made to compare different data set as random trial. I need to learn that .help needed.

03 July 2020 9,598 4 View

How do I perform Pharmacokinetic study through computational softwares? Is there any online server or any freely available software for it?

I need to perform QSAR and pharmacokinetic study in silico. Please guide me with any server or software which i can freely access and which is quite reliable as per results are concerned.

17 December 2015 301 12 View

Which metals ions form complex with sodium potassium tartrate?

Can +3 cations form tartrate complexes?

25 October 2015 3,094 3 View

How might I calculate Guanidinium concentration in molecular dynamics simulation of proteins?

Hi everyone!! While performing the MD simulations on proteins and studying their unfolding by Guanidium, How should one determine the guanidium concentration with regard to the number of molecules...

29 July 2015 4,437 5 View

Is it possible to study the interaction of a ligand with DNA at different pH conditions through a molecular docking approach?

A ligand showing different effect at different pH. I wanted to study the interaction of the ligand with DNA. So how will i study those at different pH environment through molecular docking...

09 October 2014 5,874 3 View

Request for ghrelin peptide

I am writing a project and need to create at least some data pool to send my first independent project. If anyone in this research family can provide me ghrelin peptide, in very small amount, I...

01 January 1970 6,075 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