How to generate ligand (small molecule) topology file for GROMOS 54 A7 FF?

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How can extract ciprofloxacin hydrochloride disolve in water er to organic solvent such as dichloromethan or any other solvent?

I need a procedure to extract the ciprofloxacin hydrochloride from aqueous solution by using dichloromethane in detail,. I thank you very much.

01 March 2021 4,306 1 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is thr any simplest way to Sync or connect Android SQLite Database with Server using PHP and MySQL?

I need to connect my Android application Sqlite database with PHPMyAdmin mysql database to change the application data dynamically. I need the simplest way to do this this thing. Currently my...

08 February 2021 942 3 View

How the precipitation Ratio and flow Ratio effect the output of the result?

I am doing HEC HMS calibration than i want to increase simulated value and volume of the computed so that my issue is how the precipitation and flow ratio make influential that result?

22 January 2021 152 2 View

How can a researcher searching in a new field understand the new field without taking a long time?

By that I mean, for example, I was a researcher in solar cell materials, and currently, I want to research the study of evaporation in soil and water, i.e. in the processes of solving water...

10 January 2021 6,499 4 View

Bio Rad CFX96 Touch Real time PCR System?

Dear friends I would like to ask about your experience with the instrument (Bio Rad CFX96 Touch Real time PCR System) and its performance. Also I would like to know if this version need...

29 November 2020 2,166 5 View

How can I simulate the algorithm for a IEEE802.11ac MAC layer that can optimally reflect the performance evaluation and analysis?

08 November 2020 2,492 2 View

Original DECLUE python/java/c++ implementation?

Anybody working on DENCLUE/improvements? I need to know about any "working" implementation of simple original DENCLUE algorithm.

25 October 2020 3,471 2 View

Is there an implementation of original DENCLUE available?

Does anyone know of a WORKING implementation of the original DENCLUE density based clustering algorithm, and NOT its extensions? I have explored a few from github but they ain't working.Moreover,...

01 September 2020 8,917 1 View

What is the possible way to find out the common antigen in coronavirus?

As COVID-19 has shown the strain variations, various mutants, if we developed vaccination at one place, r we sure that perticular gene has not mutated take example of E-gene of coronavirus.

27 July 2020 9,934 3 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

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 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 does the injection volume impact LLOQ and ULOQ in regression analysis (LC-MSMS)?

Hello, I have run into an issue that has sparkled a debate at work: is the LLOQ/ULOQ impacted by injection volume under the following circumstances: 1) Same dilution factor of all samples 2)...

23 February 2021 9,159 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

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

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View