[gmx-users] Fwd: how to get .mdp files

[neelam wafa]

Thanks for your help


On Sat, Feb 17, 2018 at 12:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>> 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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