Recommendations on CO2 Resistant Rocking Shaker?

A certain protocol we have developed requires the use of a Rocker/Rocking Shaker in which our dishes with cells are maintained in the incubator. The rocking is essential to the protocol but we...

09 February 2021 3,291 1 View

Do you consider it is important to vindicate Spanish as language, in scientific issues and publication of scientific articles?

03 February 2021 3,756 4 View

How to calculate the difference in the electron density of a dimer and its monomers?

Hello, I need to calculate the difference of the electron density of a dimer and the the sum of its monomers. I tried G09 without success, even using nosymm in all calculations. The problem...

15 January 2021 9,537 3 View

How to interpret hierarchical regression when a predictor is no longer significant after new variables are added?

Hello everyone: What does it mean when a variable is significant in one step but then in the next step it's no longer significant? For example, in this article...

29 November 2020 7,354 3 View

How to estimate the optimal cutpoint for a binary outcome in python?

Hello everyone, I have a dataset of diabetic patients which has been used to train an xgboost model in several outcomes such as stroke, amputation, and more. Originally we used the continuous...

21 September 2020 4,970 3 View

How to perform power analysis for a one-way ANOVA in R when treatments variances are not exactly the same?

Hi! I've been trying to perform a power analysis for a one-way ANOVA in R using the pwr package. The equation that is employed for this is based on Cohen's f and assumes that variances among the...

16 September 2020 6,098 3 View

How do you find the electrons that occupy a particular orbital in VASP?

I think this question has already been presented here on this forum, but I was not very clear. I'm running VASP calculations involving a mixture of transition metal atoms like Fe, Mn and Co in...

07 September 2020 7,228 3 View

Why doesn't my dbRDA show all the environmental variables considered?

I am performing a db-RDA in R using the package Vegan and the function capscale. I have taken into account 24 environmental factors but the program only considerate 7 of this factors. I have 54...

26 August 2020 919 6 View

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05 August 2020 9,805 2 View

How to give to an image color a single representative value?

Hello, I am trying to associate the color of an image to a single numerical value. Images (see attach) correspond to different aloe samples that change in color according to the degree of...

15 July 2020 192 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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 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

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

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

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View