How to check whether the protein bind first or the membrane using MD simulation?

I have a system with two proteins and a membrane as following protein-1, protein-2, and membrane bilayer. I would like to know whether the protein-2 binds first to protein-1 or the membrane to...

06 July 2018 9,903 1 View

How to validate a homology model?

I would like to validate a homology model. After peroforming MD simulation, one way is to check the stereochemical quality, Ramachandran plot, dssp, B-factor, etc and map the model with the...

06 July 2018 6,108 11 View

How to set gradient background in VMD in .vmdrc file?

I would like to set the default background in vmd as gradient. Therefore I tried the following method to set default background gradient in ~/.vmdrc file but that did not work. Could anyone please...

05 June 2018 9,681 2 View

Problem with VMD 1.9.2 in Ubuntu 16.04 when the representation changes to new cartoon

I have installed VMD 1.9.2 on Ubuntu machine and when I try to change the representation from lines to cartoon the GUI becomes very slow and one can feel like VMD is not working. It does not slow...

07 August 2017 495 10 View

What could be the correct 3 letter code for sulfonated tyrosine?

Is there anything like universal 3 letter code for sulfonated tyrosine like other usual amino acid residues

07 August 2017 4,076 2 View

Regarding hydrogen bond analysis in GROMACS?

07 August 2017 1,392 4 View

Histidine protonation prediction

Suggestions regarding Protonation prediction servers apart from H++., PDB2PQR and Reduce!

04 May 2017 3,011 4 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 find out the problem of VMD software when i run it?

Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...

22 February 2021 8,211 3 View

Build an orthogonal box in ASE?

Hello, I was wondering the best way to build an orthogonal box filled with a defined crystal structure in ASE. I know it could be easily done in LAMMPS, but I guess it is also doable in ASE. The...

21 February 2021 5,899 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

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