Amol Tagad

8 Questions 7 Answers 0 Followers

Questions related from Amol Tagad

How to make the force field for cationic system such as benzene dimer cation?

Hello, Anyone can suggest me how to make the force field for small cationic system.

03 November 2023 3,552 2 View

Why does in a BOMD simulation, run multiple trajectories started from started from the same initial structure, exhibit exact identical trajectories?

When I perform Born-Oppenheimer Molecular Dynamics (BOMD) simulations of small organic clusters using the CP2K software in NVE condition, I notice that running multiple simulations from the same...

31 October 2023 5,089 3 View

How to calculate fraction of alpha helics of a specific region of protein in gmx?

I want to calculate the conversion of alpha-helics to coil shape of the specific part of protein. Please anyone can suggesting me how to do in gmx? Thanking You in Advance

30 July 2023 5,006 0 View

How can I create a trajectory from the generated trajectory in Gromacs that only includes solute and solvent molecules inside the cutoff of 0.35nm?

I want to generate a trajectory using my MD data that only contains solvent and solutes that are smaller than the 0.35 limit. I make the index file of those residue. From one frame to the next,...

06 July 2023 4,337 2 View

To make the amber or charmm force field of novel molecule?

Dear Researchers, I am doing molecular Dynamic simulation using GROMACS software. Currently i am working on the sugar modified double stranded DNA, for which i need to generate a force...

07 June 2023 3,908 2 View

What does it mean when the periodic image distance is zero?

I calculated the periodic image distance of one strand in double helical DNA here, and it shows zero distance, which I don't understand. Could anyone please assist me?

09 February 2023 9,689 1 View

How to fix the problem about segmentation fault?

Hi everyone, I am new gromacs user. I am doing the MD simulation of protein-NA. I did the Energy minimization step, NVT, NPT equilibration. after equilibrating the system i submitted the...

22 August 2020 8,036 4 View

Anyone can help me for How to solve the dangling problem in DNA?

Hi, I working on Molecular Dynamics simulation of DNA. I want to study the 5'phosphate attached to thymine 16 number residue in my pdb file. I added these 5' Phosphate attached thymine in...

09 March 2020 8,379 1 View