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

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

Can the Dunn's test be used as an appropriate post-hoc for the G-test?

Research Question: Are red grouse (Lagopus lagopus scotica) a statistically significant proportion of raptor (bird of prey) diets? I am planning on using a series of G-tests (determining whether...

23 February 2021 5,827 3 View

What low-cut filter (high Pass frequency) to be used for response spectrum (Tripartite plots) ?

What low-cut filter (high Pass frequency) to be used for the response spectrum (Tripartite plots)? I am currently working on differentiating between hard/soft site responses in Indo-Gangetic...

21 February 2021 9,273 2 View

Where can the fault diagnosis data set of lithium battery be found?

Most of the data sets on the network only contain good information about the voltage and internal resistance of lithium batteries. The data of faulty battery is missing. Who can help me, I will be...

21 February 2021 8,659 1 View

How to define the sink temperature and film coefficient?

Hi, everyone. I am considering the heat conviction during compacting simulation by Abaqus. I was wondering that how to define the sink temperature and film coefficient? Is there any references...

21 February 2021 6,197 1 View

How to discriminate between Sentinel-2 Level-2A Product Discriminators?

According to the Sentinel-2 user guide here (https://sentinel.esa.int/web/sentinel/user-guides/sentinel-2-msi/naming-convention), the compact naming convention is arranged as...

21 February 2021 5,919 9 View

Are ZnS nanoparticles moisture sensitive?

Hello Everyone, I tried to form ZnS nanoparticles using the hot injection method and was able to form the same (confirmed by XRD). When I centrifuged, after the reaction I got a kind of white...

17 February 2021 1,709 3 View

Can anyone suggest a software for running a plant tissue culture lab?

A software which can help to design the experiment, store data, update new data, set subculture reminders, barcoding etc. Like Invitrosoft.

17 February 2021 3,015 5 View

Is an encrypted dataset with Microsoft SEAL compatible with Cloudsim simulator??

Hello, I would like to do homomorphic encryption using Microsoft SEAL on my dataset and then use it as an input to the Cloudsim simulator to do clustering on. Is it possible and compatible with...

16 February 2021 3,915 1 View

How to evaluate unsupervised clustering metrics when some elements do not have a cluster label in the result?

I run algorithms like HDBSCAN and MeanShift, and compare them with K-means and GaussianMixture. The first two algorithms do not return cluster labels for some elements in the dataset. My question...

27 February 2021 428 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 combine two geometries in LAMMPS ?

I am trying to simulate contact angle of water on a quartz slab using LAMMPS. I have created and equilibriated the quartz slab and the water cluster separately. Now I want to create a composite...

17 February 2021 5,884 2 View

How can I use Permanova to analyze individual variation with RNA seq transcripts and multiway Anova design?

I have a dataset with 96 individuals and 1496 transcripts of interest. I have analyzed the experiment by multiway ANOVA in the Permanova platform of Primer-E. I am satisfied that I have figured...

13 February 2021 7,217 4 View

How is KNN different from k-means clustering?

machine learning

09 February 2021 8,757 9 View

The objective is to perform clustering between normal people and hypertension people by using voice samples. How to proceed for this?

I have extracted MFCC, Chroma features from the dataset. Can anyone help me to tell what should be next step?

03 February 2021 5,536 6 View

How, if at all, can R scripts/packages be used to perform cluster analyses and motif analyses on digital trace data?

02 February 2021 728 3 View

Are there well-established collaborative sorting tasks/datasets?

Hi, I am currently working on research on communication behavior in Mixed Reality. I am planning a study, where dyads perform a task, in which they have to collaboratively cluster or sort cards...

31 January 2021 4,979 3 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

How to extract peak coordinates from a given cluster with MATLAB as in the SPM results viewer?

Hello everyone, I am trying to extract peak coordinates from given clusters in an 3D fMRI group image, e.g. a thresholded ICA z-score map. Using MATLAB/SPM I am able to extract a single peak...

26 January 2021 7,672 2 View