How can we construct a super cell of any compound from a single cell in Gromacs?

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How can we modify a force field to use it in Gromacs?

I am try to convert the .pdb file of hydroxyapatite into .gro and ormat using the command pdb2gmx. I have tried all possible force field but all are giving the same error i.e. "Fatal error:...

09 October 2015 3,790 4 View

Can we costruct Hydroxyapatite surface in Gromacs or any other Molecular Dynamics Simulations software?

I am interested in constructing the Hydroxyapatite surface. Then by cutting the surface at different angles/Planes i have check the adsorption. Is is possible to do in gromacs or I should use some...

04 May 2015 2,473 3 View

How can I get the PDB file for hydroxyapatite structure?

Can anyone tell me that how can I make hydroxyapatite structure in GROMACS-5.0? 4?

03 April 2015 3,689 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

Xiaoquan (Chris) Sun

Do you want to extend your cell to a bigger one? I just wrote a tutorial using VMD to do this. Please check at https://sunxiaoquan.wordpress.com/2015/05/12/using-vmd-to-extend-cell/.

Michal H. Kolář

Gromacs has a tool genconf. You may wish to try it with -rot or -shuffle options.

Rakesh Gupta

you may use genconf with -nbox option.