How to perform adsorption simulations in Gromacs?

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How to install VMD in ubuntu (Windows 10)?

I have already installed GROMACS in ubuntu (Windows 10), but now I would like to install VMD software in ubuntu (Windows 10), unfortunately I haven' t achieve it.

22 September 2020 9,892 3 View

Which software would you recommend me to use between GROMACS and NAMD?

I have a system where there is a protein that interacts with different surfaces (copper and graphite). I am interested in adsorption phenomenon.

19 September 2020 2,583 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

Gas sensor response and recovery time independant of flow rate and chamber volume?

I am trying to obtain the response and recovery times for my gas sensor device. It appears the the response/recovery times are primarily dependant on the flow rate of the gas I inject into the...

26 February 2021 1,511 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

Physical-chemical formation of stalactites/stalagmites. what promotes the formation/growth of these structures?

I know, or think I do, the basic idea behind these natural structures, as from what I know they form due to water dripping from the top leaving a salt deposit behind. But started to wonder about...

22 February 2021 1,400 4 View

What are some underexplored theories and concepts in Activated Carbon as A Water Filter?

Hi, me and my team mates are currently planning to pursue the topic of Activated Carbon from Coconut as a Water Filter. And we would like to ask for your suggestions and knowledge on what specific...

21 February 2021 7,561 4 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