Hi justin, Thank you for help
With Best wishes and Regards, Rama david On Wed, Nov 28, 2012 at 7:09 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/28/12 8:08 AM, rama david wrote: > >> Hi justin thank you for suggestion. >> >> I think to Calculate the free energy of solvation of biotin, I hve to use >> the method >> as per your tuotorial >> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >> gmx-tutorials/free_energy/**index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html> >> >> Is these right or I have to do anything else??? >> >> > That is the general workflow, though the .mdp settings will need to be > modified and you will need to do both van der Waals and Coulombic > transformations. I would also assume that you will need longer simulations > and more lambda points to define the transformation, since biotin is > considerably more complex than methane. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
