Why is 0.6 nm the default value for number of contact analysis in gromacs?

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Can you suggest some plant transformation vectors that I can use for the expression of GFP/YFP-tagged protein of my interest?

I want to generate stable Arabidopsis transgenic lines expressing my protein of interest fused with GFP/YFP under the control of its native promoter. I want this for localization studies. Please...

23 January 2021 2,790 3 View

Queries regarding Antibody labelling ?

Hello Everyone. I was trying to label antibody with Cat# MO-L007 - Cystein reactive monolith series antibody labelling kit. I followed every steps that the protocol states. But in the final step...

26 September 2020 3,439 1 View

How to perform theoretical BCS fitting of heat capacity curve of superconductor ?

BCS equation corresponding to electronic heat coefficient is given to the attachment.

06 September 2020 6,110 3 View

Is it possible to plot the Magnitude response of the filter having the following Difference equation, in MATLAB?

The given difference equation is Attached. I have to plot the Magnitude Response of the Filter. I have searched a lot about these types of Difference equations, and their Magnitude response in...

08 May 2020 4,110 1 View

How to plot the Magnitude response of a filter whose Difference equation is given as follows?

The given Difference Equation is : y(n)=0.33x(n +1)+0.33x(n) + 0.33x(n-1). Please help me how to plot the magnitude response of this filter. Any help will be greatly appreciated.

07 May 2020 8,451 15 View

Can anyone please help me to shade a particular region in MATLAB plot?

I have a 2D plot. I want to divide it into different parts. For Magnitude > 0.7, I want to shade it Red. For Magnitude 0.7 to 0.1 Blue. Please suggest me how to do it. Any help will be greatly...

06 May 2020 7,845 2 View

How to Highlight some particular Points in MATLAB?

I have plotted the response of a Filter using "freqs()". Now, I want to highlight the points on the plot corresponding to Y=0.1 and Y=0.1. Please suggest me how to do it. Any help will be greatly...

05 May 2020 9,504 8 View

I need some help with the Analysis of Signal in MATLAB having atleat 19056003 Data points. But in MATLAB its showing OUT OF Memory. Can anyone help?

For the study of discrete sequence in MATLAB, having about 19056003 points, MATLAB is showing OUT OF MEMORY. Is it possible to fulfill the task in MATLAB?

21 April 2020 1,767 10 View

How do we calculate mechanical stress using VASP Calculations for Ab Initio Molecular Dynamics?

If we want to uniaxially strain a structure incrementally, and calculate the corresponding uniaxial stress at every strain point, how should we use the VASP output files for this purpose? I have...

04 April 2020 9,747 4 View

How do you model CO2 on VASP?

I am new to VASP, and I'm trying to model CO2. I was able to run the simulation and got all the output files, which I uploaded onto VESTA. However, VESTA shows that the bond length between the C...

23 January 2020 8,919 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

New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before?

Question to you and THEM, the New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before? There appears to be a core problem for...

02 March 2021 3,024 2 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

Why does intensity drops as concentration increases?

Is there any reason for decrease in fluorescence emission intensity of HSA,BSA when increase the concentration ?

28 February 2021 3,653 4 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

POlymer+DMSO solution and moisture??

What could be the reason of moisture at the sides of Vial when I am preparing my polmyer+DMSO solution for membrane fabrication? What etiquettes I am possibly missing here?

28 February 2021 6,516 5 View

Should we reduce the standard unit of length to 0.31951540592 meter ?

The reasoning behind this question is to align the ratios of the proton potential in energy per charge to the speed of light in distance per time. As these two dimensions appear to be related,...

27 February 2021 947 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

What could be reason for getting such type of graph for complex impedance in case of polymer blend films?

Its effect appears in real part of ac conductivity also. Can anyone suggest any reason behind it?

26 February 2021 3,487 3 View

Martin Klvana

Nonbonded interactions are strongly distance-dependent: Coulomb potential, 1/r**2; repulsive term of Lennard-Jones potential, 1/r**12; attractive term of Lennard-Jones potential, 1/r**6.

Some programs also use 6.5 or 8.0 Angstroms as the maximum contact distance. This typically yields the first shell of residues around the probe.