Free evolution and dynamic of amino acid analysis in GROMACS?

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Is there a way to calculate energies for all residues from a pdb?

CHARMM GUI online does a protein-protein interaction where you can measure the interaction energy of one chain with all the others. Is there a way to do this for each residue? Basically I want to...

29 July 2020 8,851 3 View

In an optical diffraction (single slit experiment) we found no photons in dark fringes that should interfere destructively, how this is possible?

we did a very simple experiment of optical diffraction (single slit experiment) with a laser diode and observed dark-bright fringes on the plane of diffraction experiment (details of experiment...

13 March 2020 3,198 3 View

Which book is better to study the mechanical engineering design course?

Which book is better to study the mechanical engineering design course? What is your suggestion about a reference to teach the students?

12 March 2020 5,889 9 View

What kind of ceramic and metal are proper to make a FGM?

As you know, FGMs usually include metal and ceramic. Also, These materials have been used in high temperature environments. Based on the references, there are few temperature dependent materials...

23 February 2020 6,807 4 View

Spatial Prediction of Categorical variables with ANN model in R environment?

I would like to predict soil classes with artificial neural network (ANN) in the R environment. I train my model with neuralnet package. When using the predict function, I will only get the...

15 February 2020 4,020 3 View

How can one learn about the effects of an organic substance on the human body?

For example, we synthesized organic matter called A, at this point we want to know its effects on the human body. I wanted to know if there was a special device for this or were they using other...

16 December 2019 2,223 3 View

if we could make artificial spin ices within superparamagnetic size range (10-30nm) how would phase transitions change? what's the effect of size?

the effect of geometrical frustration have long been studied in single domain ferromagnets known as Artificial Spin Ice typically around 200-800nm in size. but I can't find any studies that goes...

03 July 2019 9,417 17 View

Is it rational to freeze/constraint bond in absence of kb for forcefield parameter?

Hi, I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond, Mn-O bond,... formed. Now i want to do MD simulation for this functionalized nanotube. (I use AMBER99SB ff) How should...

26 September 2018 2,592 5 View

How make an index for gmx gangle?

Hi, I want to calculate the 1- angle between slab surface plane and water molecule plane 2- angle between OH vector of water and slab plane. How should i define OH vector, HOH plane and surface...

12 September 2018 2,086 0 View

With due respect, kindly let me know how to publish an article, research paper or full dissertation free of cost and in very short period of time?

With due respect, kindly let me know how to publish an article, research paper or full dissertation free of cost and in very short period of time? Kindly guide in details. Regards

12 September 2018 4,277 4 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

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

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

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Justin Lemkul

You can extract the z-coordinate of an atom with gmx traj -ox -nox -noy -z and a group of atoms with the same command but adding -com. If you restrained the atoms being analyzed, you won't see such motion. The atom(s) should vibrate in place under the influence of the restraint.

Timir Tripathi

my student rohit will help u. mail him at [email protected]

or find him on RG.