[gmx-users] Adding water to protein to start the simulation process

[Tsjerk Wassenaar]

Hey :)

I see that I never stated to run the production run... But at that point in
the tutorial there have been several equilibration runs already, so it
should be trivial to figure it out. Yet I'll add a small paragraph at the
end of the production run section.
Thanks for the interest in the tutorial. I hope it's good for you.

Cheers,

Tsjerk

On Apr 15, 2011 10:04 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:



Monisha Hajra wrote:

> Hi Justin,
>
> I am trying to follow the protocol only.
>  More than the Gromacs own website, I find
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is
> more useful.
>
>
Clearly.  This is one of many tutorials linked from the site I posted
before.

 However, I am stuck at one step which is mentioned :
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
>
> I am not able to understand how to create traj.trr, traj.xtc and ener.edr
> file. Remaining all is self explained in the previous link.
>
>
These files are output by mdrun, i.e. actually running a simulation.

-Justin

 Really appreciate any help.
>
> Regards
> Monisha
>
> > > > On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
> jalemkul at vt.edu>> ...
>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>
> >    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >
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-- ======================================== Justin A. Lemkul Ph.D. Candidate
ICTAS Doctoral Schol...
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