Hi Milinda, There are different methods to do Free energy. I am using Thermodynamics Integration method; hence if you are interested to use TI I am willing to guide you, but I never use bar method. I did some parametrization so if you float your topology and mpd files I will give you some idea how to do it.
Cheers, Emmanuel ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Saturday, May 05, 2012 12:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Help with free energy Please keep all correspondence on the gmx-users list. I am not a private tutor and you have better odds of solving your problem by allowing others to provide input. On 5/4/12 8:01 PM, Milinda Samaraweera wrote: > Hi Justin > > Im a very new to using Gromacs. I tried to reproduce the values in shirts > paper > for methane. And using a similar model for study the hydration of Anilinium. > If > I send you my input files could you please take a look and give me some > suggestions. > Were you able to reproduce the methane hydration value? Aniline and anilinium are different, with the latter being more difficult to deal with on account of its charge. If you post your topology, perhaps someone will have some tips on how to modify it to produce better results, but proper small molecule parameterization is not a task well-suited for new users. It may take considerable time and effort to derive a high-quality topology. For general advice, consult: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
