[gmx-users] Fwd: how to get .mdp files
jalemkul at vt.edu
Sat Feb 17 13:45:11 CET 2018
On 2/16/18 9:04 PM, neelam wafa wrote:
> ---------- Forwarded message ----------
> From: "neelam wafa" <neelam.wafa at gmail.com>
> Date: 17 Feb 2018 00:57
> Subject: how to get .mdp files
> To: <gromacs.org_gmx-users-owner at maillist.sys.kth.se>
> 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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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