[gmx-users] RE: mdp files

[jolander at rci.rutgers.edu]

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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