We are using the same .mdp input file as they are provided in the Martini website. We don't understand what is wrong with us. However, we are trying to contact them.
Once again thanks for your reply. 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
