[gmx-users] Re: gmx-users Digest, Vol 54, Issue 15

[sudheer babu]

Thanks Justin for the response and clear explanation about water models.
This link ( http://en.wikipedia.org/wiki/Water_model ) tells that SPC water
model has 109.47 degree,  so TIP3P angle is relevant to physiological
solvent. In AMBER also mostly TIP3P water model is using rather than SPC.
I am using opls-aa FF, to this force field which water model give better
results?

Thanks in advance

> 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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> --
> ========================================
>
> 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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> End of gmx-users Digest, Vol 54, Issue 15
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