How can I find representative structure for PCA free energy landscape?

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The difference between an implicit and NPT simulation is way to high. What could be the explanation?

We perform MD simulations with Amber on a protein dimer in different circumstances. In implicit solvent on 350 K the dimer dissociates after 2 ns, while in water box, NPT run it is still stable...

16 April 2018 1,314 3 View

With what can I quench Pacific blue fluorescence?

I would like to do a fluorescence quenching experiment, but I can not use FITC and trypan blue. Has anybody got any experience in quenching the fluorescence of other dyes, like Pacific blue,...

01 September 2014 8,169 3 View

Do academic marketing and altmetrics have any (positive) influence on research evaluation?

I do not think of using social media especially built for academics (academia.edu, RG), but those of the "common" type like twitter and fb. Increasing visibility of your research through...

27 April 2014 9,078 5 View

Can someone advise on an opinion that co-authorship is a currency?

I want to apologize in advance; this will be a somewhat long post with some personal thoughts wrapped in questions. I'm not (so) far from completing my PhD and I started to think about building...

27 December 2013 5,316 8 View

Radiation absorbation with nanotechnology in space crafts

I know that Pb is the best element for absorbing radiation. But this element is heavy. So I am thinking about nano technology. Maybe with a new molecule structure or hibryd structures we will...

01 January 1970 8,013 5 View

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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 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

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Riaz A. Khan

Followings can be helpful:

Article Free-energy landscape, principal component analysis, and str...

DOI: 10.1016/j.jmgm.2009.01.006

DOI: 10.1002/prot.20310

Article Principal Component Analysis of Non‐Equilibrium Molecular Dy...

DOI: 10.1016/j.bbrc.2016.05.112

Article Relation between Free Energy Landscapes of Proteins and Dynamics

10.1063/1.5089636

Szövérfi János

Thanks for the answers, I solved the problem.