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

[Mark Abraham]

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