What are the best libraries or programs to perform network analysis of MD simulation trajectory for discovering allosteric effects?

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How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 2 View

How to arrange coordinates and extract climate dataset out of MPI-ESM-MR netcdf files?

Have a nice day everyone, I'm stuck in extracting datasets out of MPI-ESM-MR netcdf files because the latitude ranges from -3*10^6 to 3*10^6 and longitude ranges -5,9*10^6 to 5,9*10^6. Plus, the...

28 February 2021 912 3 View

Why am I getting 'Infinity' and 'NaN' in my mixed-mode energy release values?

Hi everyone, I am currently running a mixed-mode simulation of a DCB using a user-defined cohesive zone model (UEL), however, the results I am getting don't make sense. I used the same UEL for...

24 February 2021 4,157 1 View

Efficiency of Proximity Feed Patch Antenna ?

Greetings to all of You! I have searched some research papers for the designing of a proximity coupled patch antenna. Researchers are talking about the impedance bandwidth of the antenna but...

24 February 2021 7,662 3 View

Do I need to ask permission to use pictures for my questionnaire?

I would like to use some photo from a government website for my questionnaire. But, different photo is from the different owner. So, should I just get permission from that government body or still...

23 February 2021 1,631 3 View

Is there association of SARS-CoV-2 infection rate with meteorological factors?

There are contradictory research papers about the correlation between meteorological parameters and incidence of COVID-19 in some countries worldwide. Is there correlation between the...

15 February 2021 5,806 2 View

Which material, solution and reagent are needed for HPLC technique?

Of course, there are verity of material, but i need essential material and buffers for this technique. maybe there are some condition for reagent selection that i dont know them. Thank you!

17 January 2021 2,823 13 View

How can I find surface area of a pot which its top and base diameters are 34.5 and 32 cm and its height is 32 cm?

I am measuring the crop water use (ET) by using pots and lettuce crop as plant material, all the data of daily weighted pots are ready but I want to find the surface area of each pot. Can you...

12 January 2021 2,482 4 View

How can I get surface area of a pot which its top diameter is 34.5 cm and 32 cm its base diameter and its height is 32 cm?

I am measuring the crop water use (ET) by using pots and lettuce crop as plant material, all the data of daily weighted pots are ready but I want to find the surface area of each pot. Can please...

12 January 2021 1,726 3 View

Do the freezing reduces the efficacy of the cells for the electroporation ? should i decrease the voltage for the next time?

I'm making reprogramming of MEFs experiment and I used Piggy bac, Sleeping beauty and episomal transposition systems. After electroporation i froze the cells, then i thawed the cells but there...

06 January 2021 5,467 2 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?

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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...

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Ayaz Anwar

Hi, first thing is that there is no such thing as "best", it depends on multiple aspect and your choice.

There are few libraries written in python that you can use to do Network analysis like MD-TASK (MD-TASK — MD-TASK 1.0.1 documentation), Networkx (Software for Complex Networks — NetworkX 3.1 documentation), and ProteinGraph (proteingraph · PyPI) etc.

If you are comfortable with R, there are other packages that you can also use.

Read the docs, and I hope you can find something that suits your need.

Ibrahim M. Ibrahim

Ayaz Anwar thank you for your help. i think md-task provides what I need.