Maleesha T. Fernando

3 Questions 3 Answers 0 Followers

Questions related from Maleesha T. Fernando

Why does GROMACS identify stem residues in the RNA tetra-loop inconsistently?

I am performing molecular dynamics simulations on RNA tetra-loops. I have one tetra-loop with the sequence gcUACGgc (5'-3') where the stem residues are the lower case letters and the loop residues...

07 August 2025 5,005 0 View

How to convert a .gro file to .xyz file?

Hello everyone, I have conducted a MD simulation on a RNA tetra-loop in GROMACS. I have place the molecule in a large box to regenerate gas phase conditions. Now I need to convert the final .gro...

29 July 2025 7,702 1 View

How to resolve the gaps in Charmm27 forcefield for RNA molecules?

I am currently trying to perform MD simulations on a pronated RNA tetra-loop in gas phase using GROMACS. I have noticed that rna.rtp file of Charmm27 ff have not described the terminals clearly....

11 July 2025 1,373 2 View