Is RMSD enough to access the stability of the complexes?

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How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

Is there any effect of different colours of light (white, red, yellow, blue etc.) on the rate of photosynthesis? If yes, why?

Light is inevitable for the process of photosynthesis reaction. Naturally sunlight plays the vital role for this process. Light may be of different colours like white, red, yellow, blue etc....

02 March 2021 7,890 2 View

How does Scientist/RG community evaluates a case study article and the impact of it on a researcher career?

An article that is published as a case study in the SJR listed journal. How much value is added to a researcher career? How it is evaluated by a scientific researcher/University admission...

02 March 2021 9,661 3 View

What kind of food stuff increase the potentiality of human brain?

There are different kinds of food stuffs which we intake daily according to our requirements. Carbohydrate, protein, fat, mineral, vitamin, water are mainly working for the growth and development...

01 March 2021 831 2 View

What is the difference between L1 and L2 regularization in machine learning?

L1 and L2 regularization

28 February 2021 4,187 3 View

What are the application of Fixed points thoery in Chemistry.?

It is said that fixed point theory has lot of applications not in the field of mathematics only but also in various areas. So I am looking for applications in Chemistry only..

26 February 2021 3,533 1 View

How to add missing citation?

Dear colleagues, I have found that many authors have a concern regarding their missing citation in RG because often citation in RG is lower than google scholars. I also missed some citation...

26 February 2021 928 6 View

Can anyone suggest me the best way for Regression analysis of Accidents?

Dear Altruist, I want to make a regression analysis based on accident data. But I am not finding the necessary information about what type of regression is more applicable for analysis accident...

23 February 2021 9,956 3 View

How much cell pressure and back pressure should I apply to start for triaxial test for different types of soil?

We have recently purchased a triaxial test instrument (MATEST) for testing different types of soil. After installing software, we are facing a issue of saturation where the samples does not...

23 February 2021 7,194 4 View

How to assure whether a regression tree overfit or not by seeing bias-variance value of the model?

Lets consider a regression tree in which variance is 1.1065*e-10 and bias is 2.962e-13. Also the model RMSE on training set is 1.5e-5 and on training set is 1.2950e-5. Is the model is overfit or...

22 February 2021 7,755 2 View

How can I make a center of mass vs time graph?

I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...

04 February 2021 5,774 1 View

What is the best way for mobility estimation in GROMACS?

I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...

19 January 2021 531 3 View

Does GROMACS gmx trjconv sometimes leave a split in a protein?

I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein...

30 December 2020 849 4 View

CHARMM22/CMAP vs. CHARMM36?

I'm currently running a protein simulation on GROMACS. I was originally using CHARMM22/CMAP for the simulation, but with some reasons I decided to switch to CHARMM36. The thing is, I expected...

10 November 2020 8,906 1 View

How to choose the right protein subunit for symmetrical docking?

Recently, I have been dealing with symmetrical docking of protein complexes and I have a problem. Well, I have no problems with docking complexes with cyclic symmetry, it is double-walled symmetry...

09 May 2020 4,424 3 View

How to interpret the GROMACS MD Simulation RMSD Graph?

Hello brilliant researchers! After virtual screening, I performed MD Simulation via GROMACS to check the stability of the protein-top hit complex by following this tutorial...

26 December 2019 2,228 8 View

How can I measure the cluster size between center of mass?

I need to measure the aggregation of a type of molecule. The aggregation will happen if the COM of molecules becomes less than 0.85 nm. I think I should use g_clustsize but it normally calculates...

11 December 2019 2,207 4 View

How to interpret the GROMACS MD Simulation RMSD Graph?

Hello brilliant researchers! After virtual screening, I performed MD Simulation via GROMACS to check the stability of the protein-top hit complex by following this tutorial...

11 December 2019 5,952 4 View

How to calculated RMSD, of protein-ligand complex in gromacs?

Dear researchers I have performerd a protein ligand interaction using gromacs but I am unable to do the RMSD and other analysis of the protein+ligand complex for comparing it with only the Protein.

10 November 2019 7,161 5 View

How can I create SSE(secondary structure element) from YASARA trajectory file?

I was run 100ns MD simulation for native and mutant structures. Although, RMSD, RMSF plotting was done but I want to compare native and mutant structures through secondary structure element...

08 September 2019 6,145 6 View