Quoting Nancy <nancy5vi...@gmail.com>: > Hello, > > I am new to Gromacs, but have prior experience with MD simulations. I'd > like to setup and run a simulation of hydrated > dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature > (~298 K). Are there tutorials that provide step-by-step instructions on how > to do this? >
Not directly, but there are several resources available. Step 1 should certainly be Chapter 5 of the manual, to understand how to construct the topology of your system, since pdb2gmx will not do it for you. Other than that, there are general references online: http://oldwiki.gromacs.org/index.php/Membrane_Simulations There is also a plethora of question/answer threads in the list archive, which can be searched through the online interface: http://oldwww.gromacs.org/swish-e/search/search2.php Structures and topologies can be downloaded from a number of research group webpages, many of which are cited in the literature and mentioned in the archived discussions. -Justin > Thank you. > > Nancy > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
