29 June 2023 1 5K Report

Hi all,

May I know how to calculate the persistent length of a peptide using MD simulation trajectory ?

Thank you in advance !

More Kalindu Fernando's questions See All
Requesting protocols (96 well plate) for superoxide radical scavenging activity and hydroxyl radical scavenging activity?

Hello everyone, I am currently working on the natural colour pigment, betalains. I am looking for 96- well plate adopted assay protocols for measuring superoxide and hydroxyl radical scavenging...

03 January 2021 2,414 2 View

Any good reference that links economic/industrial policy to changed agent behavior?

Usually industrial policy is interpreted as changing economic structure from in favor of more productive/advanced economic activities. But would like to read something that discusses the...

31 December 2020 3,199 3 View

How to simulate the magnetohydrodynamics (MHD) phenomena in COMSOL? What is the best way to learn how to use COMSOL?

I would like to simulate the Lorentz Force resulting from the magnetohydrodynamics (MHD) phenomenon in an ionic solution.

19 December 2020 8,278 9 View

RNA-Seq for the analysis of ribosomal RNA (rRNA) processing sites?

Greetings! I want to study ribosomal RNA expression and potential processing sites in bacteria. To such effect, I want to perform an RNA-Seq experiment in order to analyze potential rRNA...

02 December 2020 1,310 2 View

Problem executing MrBayes. Help?

Hi, I'm trying to run MrBayes 3.2.7 with a matrix of 37 species and 20561 nucleotides. I consistently receive the following error: MrBayes > Execute...

18 November 2020 3,867 3 View

Where could I find a list of the main journals for free-to-publish in marine ecology and marine biology fields?

I am trying to publish a couple of articles in order to improve my scientist CV...

23 August 2020 4,264 16 View

Does anyone have a protocol about growing 3D culture in matrigel in order to extract protein for Western Blot assay?

Hello. I'd like to perform a Western Blont with samples obtained from 3D culture in matrigel. I've done experiments with 3D cultures in 96 well plates in order to test drug activity, but now I'm...

27 July 2020 1,421 4 View

Whenever modelling a bullet impact using Abaqus explicit, does the bullet needs to be given an inertia? (Ofc...)/?

I am trying to simulate the impact of a 9mm bullet into a composite metal foam (steel) panel. I might ask more questions in the near future so if anyone with knowledge about the topic and free...

24 July 2020 6,478 2 View

There is an empirical o theorical relation between band gap and electron affinity?

I am working on the simulation of a solar cell and I am using a ternary compound, for the gap the "Vegard's law" applies, but what about the electron affinity? Is there a relationship I can use?

30 March 2020 7,662 5 View

How to gather bibliography from around the world, keeping reliability and coherence?

As we face a digital era that connects researchers and researches from around the world there is a tremendous amount of works available for new researchers and their projects and works. Are there...

21 March 2020 3,202 3 View

Similar questions and discussions
MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 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

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close