Anirban Paul

5 Questions 16 Answers 0 Followers

Questions related from Anirban Paul

How to calculate Bending Modulus of lipid bilayer from MD simulation?

Hello all, I want to calculate Bending Modulus of DPPC Bilayer using the method mentioned in the paper below. Here the authors have used Fourier Transform of lipid orientation fluctuation. Can...

29 June 2021 3,021 0 View

How to get structure and topology for glycosaminoglycan (GAG) of arbitrary length?

Hello all, I want to do glycosaminoglycan (GAG) simulation in Gromacs. Initial structure and CHARMM topology for short chains can be obtained from Charmm GUI glycan modeler. But I have to take...

24 December 2020 6,292 2 View

Does the distance between two atoms in GROMACS can exceed half of the box length?

Dear all, I have done simulation of two carbohydrate molecules in Gromacs with simulation box length of 6 nm. I have corrected the trajectory using trjconv with pbc mol and center flag as used in...

05 September 2020 418 5 View

How to plot Lateral Stress map from lipid bilayer simulation?

Hello all, I want to plot lateral stress map from MD simulation of lipid bilayer i.e I want to plot local stress of bilayer as a function of x and y. Is there any Gromacs module or external...

10 August 2020 3,982 4 View

How to simulate a polymer at micromolar concentration in GROMACS?

Dear researchers, I want to simulate a polymer at micro molar concentration in GROMACS. Whenever I try with simulation box of about 30 nm each side , the force is not converging. Therefore, if I...

02 August 2020 3,416 3 View