How to make a movement of Ub-attached-Helix in protein component by MD approach?

Dear gmx user I am Gromacs version 4.6.7 user. I am working on a protein which has Ub (Ubiquitin) binding domain having strong affinity for Ub. On one side, protein has ubiquitin binding domain...

08 September 2016 3,661 7 View

How to calculate "12-6 Lennard-Jones (LJ) Nonbonded" parameter?

07 August 2016 4,631 4 View

How can I resist isopeptide [C- - - NZ] bond through out simulation in Gromacs?

HI I have attached Ubiquitin (Ub) C-term Gly to N-term Lys of a substrate protein via iso-peptide bond [C---NZ] (for ubiquitination) using Pymol and Coot. But when I do energy minimization,...

04 May 2016 4,525 2 View

Regarding Protein-Zn parameter in Gromacs?

Hi 1. I have four zinc ions within one protein system. I want to use a bonded model so that they could not fly out from my protein during simulation. Is there any documentation on the parameters...

08 September 2015 498 0 View

Any advice on ligand structure alignment against ligand database?

Hi All I have crystal structure of my ligand and I need to know the similar ligand structures from ligand database. Is there any tool/server which performs ligand structural alignment for my...

08 September 2015 3,866 7 View

In Gromacs, how do I fix a problem regarding "Unknown left-hand 'cutoff-scheme' in parameter file"?

Hi I am working on Gromacs 4.5.6 and system contains protein+sol+Ligand. I have to neutralize the system by adding NA and CL but when I use parameter file ions.mdp (attached), the following...

04 May 2015 8,908 7 View

Ligand coordinates are removed after making box [protein ligand complex Molecular dynamics issue]?

Dear Scientists I want to make system for protein ligand complex for simulation study on Gromacs 4.5.6. I follow Justin tutorial...

04 May 2015 4,725 1 View

How can I refine an unusual bond in the protein structure?

I have attached flexible linker to a protein but found some unusual bonds (at attachment point 3-4 extra bonds found in attaching amino acid residue) at the point of attachment, I used coot for...

03 April 2015 735 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Timeout error!! Processor in the loop (PIL) using STM32F4 Matlab 2018a?

Dear Researchers I am trying to perform a PIL simulation using STM32F4 Discovery board and comunication serial USB TO TTL. During simulation I receive the following timeout error: An error...

01 March 2021 2,327 1 View

How to separate water from glycerol solvent in a solvent recovery vacuum distillation column?

I am currently doing my third year design project. I have been assigned to design a glycerol recovery column in vinyl acetate monomer production. The process unit before the recovery column is an...

01 March 2021 9,525 4 View

What is the state of the drug inside solid lipid nanoparticles (SLNs)?

I am a little confuse with the mechanism of solid lipid nanoparticles (SLNs). The main point of encapsulating drugs into SLNs is because some drugs have low solubility in water. Therefore, SLNs...

01 March 2021 3,703 3 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

Can polymer concentrations be calculated based on the number average molecular weight?

Hello, I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as...

28 February 2021 7,882 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

Does different dilution factors affect negatively on NH3 reading ?

I have a sample of treated water sample & asked to obtain ammonia conc. in sample using a machine with 5-25 ppm detection range. However, upon testing with different dilution factors, all...

27 February 2021 8,483 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