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

[Justin A. Lemkul]

sudheer babu wrote:
> 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?

You will have to search the literature to find that answer.  I know I have seen 
some studies comparing water models, but I can't recall their exact citations. 
I would suggest looking up the original parameterization of OPLS (and subsequent 
modifications), and use whichever water model is specified there (which I 
believe is TIP3P or TIP4P).

-Justin

> 
> 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 <http://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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-- 
========================================

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

========================================