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:
dx.doi.org/10.1002/prot.22711
-Justin
Thank You,
Majid
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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