Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure
it
works) using l-bfgs integrator. When I run in the .trr output file, ends of dna
only move slightly towards cnt, but it doesn't wrap around it. Could anyone
please guide me what can be the possible issues here, and how can I improve it?
Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for
md simulations.
Thank You,
Majid
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