[gmx-users] GROMACS OR NAMD

[Shima Arasteh]

 :)

Thanks dear Peter.



Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, July 28, 2012 2:16 AM
Subject: Re: [gmx-users] GROMACS OR NAMD

Among simulation people at my institution, all the other lipids people
use NAMD. This was mostly a user-experience decision. When they started
their work, NAMD had better parallelization (this was before Gromacs 4+ 
came out). Now even though Gromacs has great parallelization, they don't
see a reason to switch to Gromacs because they like retaining a more "plug and
play" type of experience; although from a science perspective, this raises
questions about how rigorous they have validated their setups over time.

When you have a frontend like VMD that ties directly into NAMD job submission,
a lot of people like that, instead of tweaking all the parameters by hand.

However, NAMD isn't entirely opensource, at least not like Gromacs is (you
have to sign an EULA to use NAMD). For some people that can also be an
issue (if they are programmers do they want to be beholden to University of 
Illinois intellectual property management if they want to access or modify
the NAMD source code?)

The Formula 1 (or kit car) vs. station wagon (I guess nowadays it's all about 
minivans and crossover SUVs, isn't it? :) analogy is pretty apropos for the 
comparison between Gromacs and NAMD, respectively.

On 2012-07-27 11:20:54AM -0400, Justin Lemkul wrote:
> 
> 
> 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
> 
> -- 
> ========================================
> 
> 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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-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
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