How do I calculate tow proteins residues (Martini models) contact map in gromacs tools? Or could any one give me any script file to solve this issue?

Hello, I am looking for Gromacs utility that can be useful for the analysis two proteins or more proteins contact points in Martini coarse-grained simulations. Or any script file which can be...

03 April 2018 2,849 0 View

How can I set protein on the top of lipid bilayer (not insertion) for gromacs?

top of bilayer planer

02 March 2018 6,569 1 View

what is the simplest definition of ion exchange capacity

What this unit identifies for the ion exchange capacity ca. 0.92 meq. g-1. I am a newcomer in the membrane area. I just started. I highly appreciate your help

08 May 2021 0 0 View

what is the simplest definition of ion exchange capacity

What this unit identifies for the ion exchange capacity ca. 0.92 meq. g-1. I am a newcomer in the membrane area. I just started. I highly appreciate your help

08 May 2021 0 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

Dapi fluorescence protocol for colon cell lines ?

28 February 2021 2,534 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

Cloudy/high background western blot - can anyone help me?

Hi everyone! I try to detect VDR protein (~48 kDa) using Western Blot. After SDS-PAGE using 10% MP TGX Stain-Free Gel from BioRad I transferred the protein onto an metOH activated PVDF membrane...

23 February 2021 6,266 3 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

Protocol for membrane extraction E. coli?

Hello! I am interested in determining whether a poly-unsaturated fatty acid I have engineered E. coli to produce is being incorporated into the membrane of the cells or if it is simply a free...

21 February 2021 7,447 2 View