Subhadip Basu

7 Questions 9 Answers 0 Followers

Questions related from Subhadip Basu

How to calculate long-range interactions using GROMACS?

gmx energy module can be used to calculate short-range LJ and coulomb interactions between molecules. Is there any way to obtain long-range corrections using GROMACS?

16 December 2024 3,455 2 View

Why is 0.6 nm the default value for number of contact analysis in gromacs?

Is there any specific reason behind the choice of default value of 0.6 nm for number of contact analysis in gmx mindist module?

01 December 2021 641 2 View

Can I calculate Binding free energy from adsorption kinetics plots?

I want to get information about binding free energy of protein during adsorption process. can I calculate it from adsorption kinetics plot?

05 January 2021 1,558 3 View

How to calculate dipole dipole interaction in MD Simulation?

I want to calculate dipole dipole interaction energy between two proteins. I know their dipole moments. Is there any way to calculate the distance (magnitude and the unit vector along the...

02 May 2020 436 0 View

Can I use gromacs order to compute tetrahedral order parameter of water?

I want to calculate Orientational tetrahedral order parameter of water. The output of gmx_hydorder is confusing. can I use gmx_order instead?

18 January 2020 6,827 4 View

How to add force field parameters in Materials Studio?

I want to add CHARMM force field parameters in materials studio discover/forcite tool. Can anyone suggest a way to do that?

04 October 2019 745 1 View

What model should be used for exafs data fitting of hydroxyapatite?

I am trying to fit Sr K edge exafs data of Sr-substituted hydroxyapatite. I want to know about the choice of fitting parameters for the scattering paths. In particular, should I choose atom and...

12 February 2019 6,283 6 View