[gmx-users] GROMACS OR NAMD

[Justin Lemkul]

On 7/27/12 10:58 AM, Shima Arasteh wrote:
> Thanks dear Mark for your reply.
> It was just a simple question, liked to hear answers from the one who knows more about the simulation packages more than me. Again thanks dear Mark.
>
> In my own, I've only worked with GROMACS and don't have any experiences of NAMD.
>
> About the problem which I want to define by simulation (simulation of a protein in lipid bilayer and studying its ion conduction) , both NAMD and GROMACS are applied but I've not got the real advantages of any one over the other.
> If anybody knows an advantageous article in this about would be appreciated if suggests me.

I doubt such a thing exists, as there are no universal standards for what makes 
one simulation package better than another.  As Mark said, it is really 
user-dependent.  That requires you to read the respective manuals for what 
features and optimizations may be available.  Assuming that either simulation 
package has the algorithms you need, then the choice comes down to which package 
you find easier to use and which may make best use of the available hardware, 
which may require you to reach out to cluster sysadmins for advice.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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