[gmx-users] grompp help

[Justin Lemkul]

On 9/26/14 12:23 PM, Yaser Hosseini wrote:
> hi gromacs user
>
> i have problem with grompp command in gromacs i cant find .mdp files
> and i cant pass step 4 in this tutorial:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html
>
> im new in gromacs please help me to find a way to fix my problems.
>

I already told you this yesterday - the tutorial gives you the file to download. 
  On that page, note the section:

"An .mdp file is normally used to run energy minimization or an MD simulation, 
but in this case is simply used to generate an atomic description of the system. 
An example .mdp file (the one we will use) can be downloaded here."

Note that the word "here" is a link from which you can download the file.  If 
you're not familiar with file downloads, text files, or examining/editing their 
content, you should probably stop with tutorial material and consider some Linux 
basics in terms of file management before attempting to do something complex 
like MD simulations.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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