<div dir="ltr">Thanks Justin for the response and clear explanation about water models. <br>This link ( <a href="http://en.wikipedia.org/wiki/Water_model">http://en.wikipedia.org/wiki/Water_model</a> ) 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.<br>
I am using opls-aa FF, to this force field which water model give better results?<br><br>Thanks in advance<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> Hi gmx-users,<br>
> I want to use tip3p water model when I mention this model with flag -cs<br>
> by genbox command it showed that no program for tip3p.gro,<br>
> from this link<br>
> <a href="http://www.gromacs.org/pipermail/gmx-users/2007-February/025712.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2007-February/025712.html</a><br>
> I understood that mention -spc water model in genbox command but in .top<br>
> file edit #tip3p.itp# so it can take as tip3p water model.<br>
><br>
<br>
There is no such option in genbox. You can specify "pdb2gmx -water tip3p" and<br>
it will automatically #include "tip3p.itp" for you, or you can certainly do it<br>
by hand after the fact.<br>
<br>
> 1.My doubt is I am mentioning -spc in genbox command but how it will<br>
> change to tip3p by simply editing in .top file?<br>
<br>
There is no such option, so I am not clear on what you are asking. Specifying<br>
"genbox -cs spc216.gro" will give an equilibrated solvent box of three-point<br>
water, which suffices for either SPC or TIP3P.<br>
<br>
> 2. From literature I found that tip3p HOH angle 104.5 degree but spc<br>
> model HOH angle 109.4 degree and it shows ideal tetral hedral shape,<br>
<br>
The angle of TIP3P should be 104.5, also. Where have you seen 109.4?<br>
<br>
> So mostly people are prefer to use tip3p rather than spc, am i right?<br>
><br>
<br>
Depends on the force field you're trying to use. For example, with Gromos force<br>
fields (which were parameterized for use with SPC), using SPC or SPC/E gives<br>
very good results in light of the original theory behind the force field and the<br>
parameterization.<br>
<br>
-Justin<br>
<br>
> Can clear me this doubt<br>
> Thanks in advance.<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
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--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</blockquote></div><br></div>