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

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 20 20:47:09 CEST 2011

majid hasan wrote:
> 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?

Energy minimization and dynamics are independent processes.  You should not 
expect large structural changes during EM with any of the methods.

> Moreover, what is the right value of nstlist for amber99sb-ildn 
> forcefield for md simulations.

Always start with the primary literature:



> Thank You,
> Majid


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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