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

[majid hasan]

Okay, thanks. But then does it make any big difference on mdrun if we don't 
minimize energy first?

And one more thing, any idea how long it may take to run md for 367 atoms on a 
laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it 
is possible to get any results from mdrun on laptop?

Thanks again,
Majid



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, April 20, 2011 11:47:09 AM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of 
dna around cnt



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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