[gmx-users] grompp help

[yaser]

thank you for replay 

when i want to download this file and i click on it its nothing happend and just the text page opend and its nothing to download.



Sent from my iPad

> On Sep 26, 2014, at 19:56, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> 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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