[gmx-users] RE: mdp files

[Tsjerk Wassenaar]

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