[gmx-users] GROMACS OR NAMD

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jul 27 16:58:06 CEST 2012

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.


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, July 27, 2012 6:28 PM
Subject: Re: [gmx-users] GROMACS OR NAMD

On 27/07/2012 9:05 PM, Shima Arasteh wrote:
> Hi,
> Does GROMACS package have any advantages over NAMD?

Yes, but the real question is which package provides the best scientific return for your time and your computer time, given your simulation problem, your hardware and your experience with each package. You don't want an F1 car to drive to the shops, and there's no point being in pole position in a station wagon. You need to read at least the most recent publication describing the newest features and performance in each in the context of your problem, before you can start grappling with the question,

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