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 <[email protected]> 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 <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
