How to solve DNA base pairing getting disrupted during simulation?

Shreya Bhattacharya @Shreya-Bhattacharya-12

20 May 2022 1 6K Report

Hello everyone,

Can someone help me with this.

I have run a complex with DNA, Protein and RNA in NAMD for 50 ns. However, after the end of simulation, the base pairing of DNA and DNA RNA hybrid completely got disrupted. What should I do inorder to get a stable DNA and RNA in simulation. I have used CHARMM36 force field. The simulation was done at 310k.

Sutanu Mukhopadhyay

You may perform MD simulation with harmonic position restraints on the heavy atoms. This allows the solvent to equilibrate around the complex/DNA/RNA without disturbing the structure. For further details, check out the NAMD manual.

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