Could anyone point to molecular mechanics force fields for selenium nanoparticles?

Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using...

11 December 2018 7,209 4 View

How to apply position restraints for carbon nanotubes in GROMACS?

I am running a system with protein and carbon nanotube using GROMACS 5.1.4. I used position restraints for carbon nanotube however, during NPT run (both protein and carbon nanotube fixed),it...

09 October 2017 1,315 3 View

How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying to simulate...

09 October 2017 4,086 2 View

Does anyone have parameters for carbon nanotube (CNT) in AMBER package format?

There are many papers on MD simulations of proteins with carbon nanotubes using AMBER force field. I was wondering if anybody can provide parameters (frcmod or lib files) for carbon nanotubes in...

07 August 2017 437 1 View

How to calculate number of Nanoparticles given wt/wt %?

06 July 2017 5,581 2 View

How to deal with water bubbles during NVT runs with position restraints in a molecular dynamics simulations??

I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...

02 March 2017 1,157 2 View

How to build (replicate) lipid monolayer systems using gromacs?

I have a pdb file of coarse grained lipid monolayer system consisting of 64 DPPC lipids. The pdb file is missing box information. I am interested in simulating nanoparticle penetration in...

01 February 2017 2,528 1 View

Simulating chitosan using Glycam force field?

Is there any publication reporting simulation of chitosan using Glycam06 force field?

11 December 2016 2,029 0 View

What is the stereoisomerism in divalen cross-links found in collagen?

I was wondering if anybody has worked with chemistry of these two cross-linkers and have characterised by FTIR or MS whether they are cis/trans or S/R isomers? Apologies: I am not a synthetic...

08 September 2016 8,568 4 View

Anybody acquainted with simulations of hydroxyapatite surfaces in AMBER?

Dear list, I am trying to simulate protein unfolding on hydroxyapatite surface using AMBER MD package. I got the parameters for HAP (based on the interface force field). I prepared the system...

07 August 2016 6,801 0 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 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

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 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 it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View