Apramita Chand

6 Questions 7 Answers 0 Followers

Questions related from Apramita Chand

Is it possible that short peptides may adopt compact conformation in urea solution and extended form in presence of protecting osmolyte?

Contrary to established research,is this kind of opposite behavior possible? Any literature on this? Any ideas how this can be possible?

17 January 2018 1,178 3 View

Which amongst the clustering algorithms in GROMACS is more fuzzy in approach?

There are several clustering algorithms in GROMACS like K-means ,neighbour algorithm,J.Patrick, Monte-Carlo, linkage. Which is closest to fuzzy clustering method ? Any references?

17 November 2017 919 2 View

Hydrogen Bond Lifetimes calculated in gromacs with and without applying pbc are different. Which value should be considered?

I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. I tried g_trjconv with application of -pbc mol -ur compact...

31 August 2017 3,343 3 View

What is the correct way of calculating hydrogen bond lifetime in GROMACS?

In gromacs ,on using -life option we get the following answer Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.149 6.692 9.313 0.00998919Backward 0.589 1.699 5.894One-way...

21 December 2016 9,966 6 View

How different is the nature of hydrogen bonding in the solid or liquid state?

Are there any references which can give specific details as to how hydrogen bonds differ in the solid state and liquid state? For instance,are hydrogen bonds in the solid state more directional?...

04 April 2016 1,959 7 View

How to proceed when GROMACS shows error in residue identification while inputing a .pdb file generated by packmol

As a beginner in gromacs,I generated an initial configuration of some peptides in mixed solvent systems. After giving pdb2gmx command for generating .gro file and .top file, an error message comes...

03 August 2015 8,427 3 View