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

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

VMD movie making of GROMACS trajectories?

While making movie of GROMACS trajectory in VMD, How one can stop motion of protein going from one direction to the other in PBC box?

08 September 2016 8,120 0 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

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

Ester cleavage conditions?

Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...

01 March 2021 8,766 3 View

How to remove DCU and HOBT from my reaction?

I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??

28 February 2021 2,153 1 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

What is the most common number of epitopes in an multi-epitope Vaccine?

hi everyone, I'm interested in the field of vaccine design specifically multi-epitope cancer vaccines , I want to know if there is a minimum and maximum number of epitopes we could use in a...

27 February 2021 3,882 3 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 increase solubility of Poly acrylic acid in Dioxane solvent?

I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...

25 February 2021 2,225 5 View