[gmx-users] Is there any fundamental difference between the output of serial, gpu and parallel gromacs run

[Sudipta Kumar Sinha]

By the way we have used same gromacs version and also tried with other additional version.

Sent from my iPhone

On Mar 24, 2013, at 6:48 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> In principle, you should be able to reproduce their results if you use the
> same GROMACS version and the same algorithm. I would check very carefully
> that I have been using the same algorithm parameters - e.g. contact the
> authors to see if their .mdp files are available.
> 
> On Sun, Mar 24, 2013 at 9:48 PM, sudipta <sudipta.mml at gmail.com> wrote:
> 
>> Hi All,
>> 
>> We were trying to test a simple lipid bilayer system using gromacs with
>> martini model and polarizable CG water to validate the model. We have
>> tested it by several ways such as varying gromacs version, precision,
>> different platform,  different initial configuration, increasing length of
>> trajectory etc. However, we were always getting exactly same results and
>> didn't reach the exact reported value as published in plos computational
>> biology, e1000810,vol 6, issue6, 2010. We are getting a small error
>> compared to their value. However, we used the same system, same model, same
>> md simulation parameter, same length of trajectory (initially then we have
>> varied). May be the authors have used MPI version of gromacs. However, we
>> have not tested with MPI version of gromacs. Is there any sources of error?
> 
> The most likely possibilities are some deviation in your attempt to model
> the method, or some difference between the code that computed the result
> you are seeking to reproduce, and the code you have been using. Nobody can
> assess the latter possibility without more detailed version and .mdp
> information, however.
> 
> Mark
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