[gmx-users] energy minimization

[Justin A. Lemkul]

shahab shariati wrote:
> Hi gromacs users
>  
> I want to study interaction of protein-dna by gromacs.
>  
> For energy minimization, is using of only 1 algorithm, for example 
> steepest descent or conjugate gradient, enough? How many steps is 
> necessary for EM?

I would encourage you to do some background reading on the different algorithms. 
  The Gromacs manual (sections 3.10.1 and 3.10.2) discusses these different 
algorithms.  The first sentence of section 3.10.2 is particularly to the point.

The number of steps required will depend upon how reasonable the starting 
structure is and what your convergence criteria are.

-Justin

>  
> 
> Any help will highly appreciated!
> 

-- 
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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

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