[gmx-users] tip3p water model
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 3 20:51:35 CEST 2008
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
> 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
> Can clear me this doubt
> Thanks in advance.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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