[gmx-users] tip3p water model

[Justin A. Lemkul]

sudheer babu wrote:
> Hi gmx-users,
> I want to use tip3p water model when I mention this model with flag -cs 
> by genbox command it showed that no program for tip3p.gro,
> from this link
> http://www.gromacs.org/pipermail/gmx-users/2007-February/025712.html
> I understood that mention -spc water model in genbox command but in .top 
> file edit #tip3p.itp# so it can take as tip3p water model.
> 

There is no such option in genbox.  You can specify "pdb2gmx -water tip3p" and 
it will automatically #include "tip3p.itp" for you, or you can certainly do it 
by hand after the fact.

> 1.My doubt is I am mentioning -spc in genbox command but how it will 
> change to tip3p by simply editing in .top file?

There is no such option, so I am not clear on what you are asking.  Specifying 
"genbox -cs spc216.gro" will give an equilibrated solvent box of three-point 
water, which suffices for either SPC or TIP3P.

> 2. From literature I found that tip3p HOH angle 104.5 degree but spc 
> model HOH angle 109.4 degree and it shows ideal tetral hedral shape,

The angle of TIP3P should be 104.5, also.  Where have you seen 109.4?

>   So mostly people are prefer to use tip3p rather than spc, am i right?
> 

Depends on the force field you're trying to use.  For example, with Gromos force 
fields (which were parameterized for use with SPC), using SPC or SPC/E gives 
very good results in light of the original theory behind the force field and the 
  parameterization.

-Justin

> Can clear me this doubt
> Thanks in advance.
> 
> 
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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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