Anirban Paul

4 Questions 16 Answers 0 Followers

Questions related from Anirban Paul

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 6,268 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 391 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 3,930 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 3,390 3 View