On 2/16/18 9:04 PM, neelam wafa wrote:
---------- Forwarded message ---------- From: "neelam wafa" <neelam.w...@gmail.com> Date: 17 Feb 2018 00:57 Subject: how to get .mdp files To: <gromacs.org_gmx-users-ow...@maillist.sys.kth.se> Cc: Hi I am new to this list. I have run the gromacs tutorial ' lysosime in water'. now i have to run a protein ligand simmulation. But i am confused about how to generate .mdp files as in tutorial they have used five .mdp files which are to be downloaded from bevanlab.biochem. These are ions.mdp, em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these have to be generated with aome software according to the protein and ligand.
There may be differences required to properly account for different types of systems, and certainly you will need to make changes to the nonbonded setup if you're using a different force field.
There's no magic to these files - they're just plain text. You could fire up your favorite plain text editor and write them from scratch, if you wanted. Otherwise, just modify existing files to suit your needs, again using nothing more than a plain text editor (vim, emacs, etc).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
