[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

majid hasan pu_majidhasan at yahoo.com
Wed Apr 20 20:43:40 CEST 2011

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,
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