Uttam Kumar Basak

10 Questions 35 Answers 0 Followers

Questions related from Uttam Kumar Basak

How to calculate Lennard-Jones parameters for a particular atom?

It is often necessary to know the parameters of Lennard-Jones (LJ) potential for various atoms. There may be database for LJ parameters. I am just curious to know how these parameters are obtained...

18 January 2016 9,686 11 View

Is there any model or equation for ridge dynamics?

I have a 2D system, you can think of it as a 2D sheet. There is a formation of ridges in this sheet when it is given a constant in-plane pressure. I want to model the ridge dynamics. Is there any...

25 July 2014 1,687 3 View

Why does fractal dimension (Fd) increase with coverage area (A) as Fd ~ A^0.15 for a sigmoidal growth?

I am studying a dynamic process where one phase (say, phase A) slowly transforms into another phase (say, phase B) and the transformation profile (i.e. coverage area vs time plot) is sigmoidal. I...

31 May 2014 5,855 21 View

How can I calculate the interaction energy between two molecules as function of their separation?

I want to calculate interaction energy between two molecules as a function of their separation. I also want to see how geometry of the molecules affects their interaction energy. Can you suggest a...

25 May 2014 1,709 16 View

Is it possible to calculate the solubility of some material in water from the free energy of solvation?

I have obtained free energy of solvation in water using perturbation method with GROMACS. I want to calculate the solubility of the molecule in water. How can I do that?

14 January 2014 5,295 34 View

Fractal dimensions(Fd) calculated using the box counting method vary depending on the grid location. Which value of Fd is most appropriate?

Fractal dimension calculated using the box counting method depends on the grid location. I have attached a file which contains the fractal dimensions obtained using ImageJ with FracLac plugin at...

06 January 2014 2,453 15 View

How can I get Antechamber working - it is giving an error message?

Antechamber from AmberTools13 is giving an error: " cannot run "..../sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" " I have installed AmberTools13...

21 August 2013 3,993 7 View

What is the best software to create an energy minimized 3D representation of a molecule in .pdb format?

I need a 3D structure of molecule for molecular dynamics simulation. I don't have a good chemistry background. I want a software which can assign the bond length, bond angle etc. automatically....

12 August 2013 6,542 10 View

Topology generated by ATB server contains a charge group of 32 atoms? Is it reasonable? How can I obtain the partial charges of atoms for molecule?

I have used ATB (http://compbio.chemistry.uq.edu.au/atb/) server to generate topology for piroxicam molecule (having 36 atoms). It has generated topology for GROMOS96 force field with two charge...

07 August 2013 2,384 6 View

How to add hydrogens into a molecule (pdb file) before its topology is calculated using ATB (Automated Topology Builder) server?

I have a .mol 3d structure of a nonligand molecule (piroxicam). I opened it in pymol and added hydrogens to it before saving it as .pdb file. Then I used this file as an input to ATB...

29 July 2013 5,011 5 View