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. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 54, Issue 15 > ***************************************** >
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