Cluster entropy distribution through gromacs?

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Multiple MD simulations through gromacs?

Dear all, I have done the long 200ns MD simulation of protein in water. I have received a comment from the reviewer that for the convergence of the results I have to perform multiple simulations...

03 April 2019 2,970 9 View

How to calculate the Preferential Interaction Coefficient?

Dear all, I am trying to calculate the preferential interaction coefficient of osmolytes with protein from COM of protein. I had tried to calculate it using gmx select command of gromacs but when...

31 December 2018 9,716 2 View

Can anyone tell what value of Temperature should be taken during the binding constant calculation after docking?

I am trying to calculate the binding constant of drug after docking through Auotdock4. Can anyone tell me what value of Temperature should be taken during the calculation? It has also been know...

11 December 2018 3,711 7 View

How to calculate the population density ?

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08 September 2018 1,981 2 View

How to calculate the number of water molecule at particular distance from the surface of protein?

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04 May 2018 3,717 7 View

Position restraints MD

Dear all, I am doing MD simulation of protein and metal atom. I have to apply position restraints on metal atom. I have applied it as follows- ( kindly correct me if i am wrong) first made an...

01 January 1970 6,939 5 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?

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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...

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

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

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

Dmitri Kireev

If one assumes that a structural cluster corresponds to a system's microstate, then S = kB Sumi(pi log(pi)), where kB is the Boltzmann constant and pi is the probability for the system to be in the i-th microstate (i.e., cluster). The probabilities can be readily calculated from the cluster populations.