How to minimize the standard deviation of protein-ligand complex using mmpbsa (CaFe 2.0 vmd plugin) using namd?

Hello, I wanted to know how can I minimize the standard deviation (SD) of my simulated protein-ligand complex of 50ns using MM/PBSA method of Cafe 2.0 plugin of VMD plugin using NAMD. I have tried...

10 December 2020 8,132 1 View

What is the configuration file for blind docking using PyRx for multiple ligands?

I am trying to run blind docking with multiple ligands and one macromolecule using PyRx but somehow i am getting poor binding affinities. What is the configuration file for blind docking in PyRx...

01 April 2019 2,132 3 View

How to deposit gold nanoparticle onto (commercial) disposable screen printed carbon?

i have carbon screen printed electrode and gold nano particles suspension in citrate buffer, how to deposit the particles on the electrode in a way to get uniform distribution?

28 February 2019 9,323 3 View

If i have protein amino acid sequence how to get the 3D structure?

i have amino acid sequence of protein and I am looking for a free tool can predict the 3d structure, also i have the aptamer of this protein and i want to know how they bind with each other ?

16 February 2019 5,364 5 View

What is the basic different between IDA and SPE?

Currently Iam working on amperometric biosensor using SPCE (screen printed carbon electrode) but I still confuse to figure out what is the different between this electrode with Interdigitated...

04 November 2018 7,738 2 View

How to design read out circuit for electrochemical sensor?

hello, iam working on an electrochemical sensor, to detect protein biomarker using DNA prob, i want to design a read out circuit for my sensor, also i want to know what is the differantce between...

03 November 2018 2,763 2 View

HMM for maternity dataset using R?

I have attached the simplified form of my data. The variable "Gender" will be the hidden state in our model and "Pregnancy Outcome" will be the observation. What is confusing me is that I don't...

18 September 2018 3,527 1 View

What is the best way to do sample size calculation?

I am conducting a research study and for sample size calculation, i chose a paper with a similar study design to enter measurements in the sample size calculator. Is it correct to choose a paper...

03 April 2018 4,846 5 View

How long does it take to reach a stable OCP value in an electrochemical cell?

I am currently working with low alloy steel in order to achieve EIS (OCP) and Potentiodynamic polarisation values. The value of the potentiable does not stabilise even after an hour of immersion...

18 January 2018 2,808 13 View

To model an ordinal response, with categorical and count variables is there anything other than Ordinal Logistic Regression?

26 June 2017 6,778 5 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

I need to image mesoporous silica nanoparticles that are in ~100 nm size and do high resolution TEM to look at mesopores. what grids should I use?

Need to image mesoporous silica nanoparticles using the TEM. Also, need high resolution TEM images to see the mesoporous structure. Kindly suggest what kind of grids to use. Thanks, Shatadru

02 March 2021 1,787 2 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does anyone know to clarify these changes?

01 March 2021 1,290 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 convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 View

High aspect ratio hexahedral mesh optimization solver?

I am interested in evaluating mesh optimization solvers that converge to high aspect ratio unstructured hexahedral grids. In other words, I am interested in a solver that optimizes warpage,...

26 February 2021 7,279 2 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