Why I couldn't obtain a gel from APTES? Does the Amine group affect the gelation process?

I am trying to make a gel from APTES as a precursor using the sol-gel reaction. I tried different solvents (ethanol, acetone, DMF) and different catalysts (basic and acidic) with different...

03 October 2020 9,673 5 View

How to estimate Lipid-Protein interactions durations from MD trajectories ?

Hi, I have trajectories of a protein embedded in an explicit membrane and water environment. I would like to estimate lipid-protein interaction durations i.e., the average duration of the...

26 October 2019 5,374 3 View

How can we separate between the fluorescent effect and second-order vibration in the wavenumber [1000-2000cm-1] in Raman Spectroscopy?

I am researching BaTiO3 ceramics and i find peaks in the wavenumber [1000-2000cm-1].How can we separate between the fluorescent effect and Second-Order vibration in the wavenumber [1000-2000cm-1]...

30 April 2019 9,125 8 View

How to read Gaussian Cube file?

Hi, I have a Gaussian cube file (.cube) that I obtained with gmx spatial. It represents the spatial density of cholesterol during a simulation (Protein in a membrane with explicit solvent). I...

21 April 2019 8,430 1 View

What is the difference between 633nm and 785nm lamp in Raman Spectroscopy?

I am researching rare earth doped pervoskite ceramics and found that most researchers used 633nm Laser. What is the difference between them and will there be much difference in the results?

15 April 2019 5,396 8 View

What is the lipid composition of the mitochondrial Outer Membrane (omm)?

Dear all, I would like to simulate a protein which is located in the Mitochondrial Outer Membrane (OMM). I was searching in the literature about lipid composition of this latter (in Mammals) but...

04 February 2018 5,094 2 View

Cyclophosphamide (Cy) and Scid mice !!

08 June 2017 536 7 View

Is it necessary to confirm the RNA-seq results by quantitative RT-PCR?

29 August 2016 1,740 3 View

How to generate a topology for a HEM protein using CHARMM 27 as FF?

Dear all, I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. Since my system is complex, I decided to start first with a monomere taking only...

11 May 2016 6,272 2 View

Fixing missing atoms and residues in PDB file before using pdb2gmx

Hello, I have missing atoms and residues in my PDB file and I need to fix them in order to proceed with pdb2gmx (GROMACS). I used swissModel but the generating file is lacking the final residue in...

09 May 2016 9,626 10 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

Can impedance of antenna be less than 50 ohms?

I am simulating helix antenna in hfss, right now, giving excitation with 50 ohms port. When I see the results of Z parameter (real). It shows lower than 50 ohms. Do not understand, if it can be...

27 February 2021 4,218 7 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