Uttam Kumar Basak

14 Questions 35 Answers 0 Followers

Questions related from Uttam Kumar Basak

What does it signify that a system has strange attractors in phase space but its motion is not sensitive to initial conditions?

If I am not wrong, a dynamical system is called 'chaotic' if it satisfies the following two conditions: (i) having strange attractors in phase space, (ii) sensitivity to initial conditions. What...

11 November 2015 7,708 8 View

Can anybody suggest anything regarding parameterization of tetrachloroferrate (FeCl4-) ion?

I need the parameters for FeCl4- ion in any of the following force fields - GROMOS, AMBER, CHARMM or OPLS. The force field development of transition metal complexes is very difficult. I did a...

04 April 2015 5,832 7 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...

07 July 2014 4,399 4 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...

05 May 2014 7,578 17 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?

01 January 2014 2,531 35 View

Which software do you use for Molecular Dynamics simulation?

I just want to take a survey. Please mention the name of the software. You may add what you are studying with molecular dynamics.

01 January 2014 10,087 8 View

What if I define a dodecahedron box of a rectangular system of solvents? What will happen to the molecules outside the dodecahedron box during md?

I have solvated a ligand molecule with water molecules within a box defined by "inside box 0. 0. 0. 33.726 33.726 33.726" in packmol. Will it be meaningful and helpful to use editconf for defining...

10 October 2013 8,890 1 View

How to solvate a ligand molecule with a non-aqueous solvent like octanol?

I want to solvate a ligand molecule with (united-atom) octanol. I have a pre-equilibrated box of 512 (united-atom) octanol molecules. I am using editconf and genbox tool for solvating the ligand...

09 September 2013 8,757 8 View

Which one of the programming language do you think is better, Perl or Python?

I have used Python. It is simple and powerful. One of the crazy things about python is ipython shell. I don't know Perl. I have heard that it is an excellent scripting language. Which one do you...

09 September 2013 7,826 11 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....

08 August 2013 787 11 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...

08 August 2013 5,200 8 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...

08 August 2013 6,806 7 View

How can I validate the GROMOS topology of Piroxicam (NSAID) generated by PRODRG server ?

I want to simulate Piroxicam (NSAID drug) molecules with GROMACS. I have the GROMACS topology file generated by PRODRG server. As mentioned here http://pubs.acs.org/doi/abs/10.1021/ci100335w...

07 July 2013 5,602 5 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...

07 July 2013 3,894 6 View