[gmx-users] RE: mdp files

[Justin A. Lemkul]

That depends on what the problem is.  It's always best to quote the 
exact error message when asking for help :-)  If you're referring to the 
use of -conc and -neutral, those were not available in version 3.1.  
It's always recommended to use the newest version of the software, 
unless, for some specific reason, you need to use an old version.

-Justin

jolander at rci.rutgers.edu wrote:
> Hi Tsjerk,
>
> Thanks for the tutorial. I was going through the steps and ran into a
> problem when placing in the ions in order to neutralize the system. Would
> this because my version of Gromacs is 3.1 and your tutorial is for v3.3.3?
>
> Thanks for the help,
>
> -John
>
>   
>> Hi,
>>
>> For a tutorial and a workflow you can also check out:
>>
>> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
>> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/01-Preparation-Workflow.jpg
>>
>> A bit in progress still, and any comments welcome ;)
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Sat, Jun 21, 2008 at 9:40 AM, Vitaly Chaban <vvchaban at gmail.com> wrote:
>>     
>>>> Special thanks to Vitaly, Mark and Justin for there comments. I've
>>>> revisited the wiki site and read through chapter 5 of the manual. I'm
>>>> currently going through the tutorial with a standard protein. I run
>>>> into a
>>>> problem when I use the command:
>>>>
>>>> grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
>>>>
>>>> The error states that the em.mdp file doesn't exists, but none of the
>>>> steps in the tutorial leading up to this command creates the em.mdp
>>>> file.
>>>> I was just wondering what step in the process is the .mdp file created
>>>> or
>>>> do I have to have that already created off to the side ready for the
>>>> grompp command?
>>>>
>>>> Thanks again,
>>>>
>>>> -John Landers
>>>>         
>>> I guess em.mdp is a parameter file for energy minimization. Look here:
>>> http://www.gromacs.org/documentation/reference/online/mdp.html for how
>>> one can make it. If you want to make an energy minimization of your
>>> system firstly, you just have to change
>>> "integrator = md"
>>> to
>>> "integrator = l_bfgs"
>>> or
>>> "integrator = steep"
>>>
>>> I have also sent you personally the ready example to start with
>>> simulating carbon nanotube.
>>>
>>> Best,
>>> Vitaly
>>>
>>>
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>>>       
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
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>>     
>
> _______________________________________________
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>   

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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