[gmx-users] TIP4P, TIP4P-Ew

[Tsjerk Wassenaar]

Hi Lin,

That tutorial doesn't really give a good procedure for production work
simulations. Use a rhombic dodecahedron instead, with a distance to
the wall (-d) of at least 1 nm. Maybe it's better to try the tutorial
I put up on http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ It's not
as good on the graphics, but the procedure is closer to what you need
for proper simulations.

Cheers,

Tsjerk

On Sun, Sep 28, 2008 at 6:16 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>
> HI
> I followed the tutorials
> http://md.chem.rug.nl/education/mdcourse/MDpract.html
>
> the procedure is
> 1. create the box
>
> Use a standard cubic box and be sure that the protein does not see its
> images. This means that the distance from the the box wall should be greater
> than half of the cut-off (1.4 nm)
>
> editconf -f minimized.gro -o minimized_box.gro -d 0.75 -bt cubic
>
>
> 2. solvate the protein
> genbox needs as input the protein in a box (minimized_box.gro) and a solvent
> box (spc216.gro) and the topology of the solute (aki.top) and of the solvent
> (spc.itp).
>
> genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p
> aki.top
>
> Is it the same thing for the TIP4P-Ew water model?
>
>
> Thank you
> Lin
>
>
>
>> Then, I can say my system is under the water model-TIP4P-Ew.
>> And, other simulation procedures are all the same for any kind of water
>> model.
>
> What procedures do you mean?
>
>
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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