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

[Justin A. Lemkul]

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

You should always run energy minimization.  What I'm saying is that you should 
not expect to see any major changes or important phenomena evolve when simply 
running EM.

> 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?
> 

You can get results, but that depends entirely upon how much of the processor is 
being used to do other things at the same time.  For a small system, running 
locally may be an option, but for anything larger than a few hundred atoms 
you're better off running on a real cluster to avoid performance loss.  It will 
certainly "work," but probably not as fast as you might need for very long 
simulations.

-Justin

> 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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-- 
========================================

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

========================================