Free evolution and dynamic of amino acid analysis in GROMACS?

More Roja Rahmani's questions See All

How show box in CHIMERA?

Hi, I did an MD simulation by gromacs and now I want to show it in CHIMERA. As CHIMERA can not read a .gro file, I converted it to .pdb but I can't see the simulation box. How can I see the...

31 December 2018 8,636 2 View

What is the difference between surface and bulk solution? Which one is more polar?

Hi, What is the difference between surface and bulk solution? Which one is more polar? does it depend on the characteristic of surface? Since ZnS surface(nano sheet) is partly hydrophobic, so...

31 December 2018 8,557 7 View

How show in ball and stick view by OVITO?

Hi, How show in ball and stick view by OVITO? Best

31 December 2018 8,262 1 View

Problems with g_dist?

Hi, my system contains 30 same molecule around nanotube. each molecule is in 2nm far from nanotube. i want to know how this distance change during simulation time. I have attached the same...

11 December 2018 5,243 1 View

How calculate adsorption number of molecule in molecular dynamics simulation?

Hi, My system contains 20 amino acids around nanotube. I want to know the adsorption amount of AA DURING simulation time; the adsorption occurs when the distance between one of non-hydrogen atoms...

10 November 2018 1,644 6 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...

08 September 2018 1,873 6 View

How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

Hi, How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation? I did simulations by GROMACS, is it...

08 September 2018 5,160 3 View

How can i calculate the distribution of water polarization above surface?

Hi, I study the interaction(calculating PMF for different distances of molecule above surface) of amino acid with surface in presence of water( using TIP3P water model, AMBER force field by...

08 September 2018 6,851 7 View

How define Mn in AMBER forcefield?

Hi, I have Mn in my strucrure and i want to use AMBER forcefield in GROMACS. But it is not defined in atomtypes. What should i do exactly? Best regards

08 September 2018 1,296 5 View

How functionalize ZnS nanotubes with different organic and inorganic molecules?

Hi, There are many studies about functionalizing different ZnS nanostructures. but i couldn't find anything about ZnS nanotube. Is it possible, at all? would you please share me your...

08 September 2018 3,161 9 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.