<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt;color:#000000;"><div>Dear All,</div><div><br></div><div>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?</div><div><br></div><div>Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations.</div><div><br></div><div>Thank You,</div><div>Majid</div><div style="position:fixed"></div>
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