Thanks David. Can you also help me with the .gro file? In general how do i set up a .gro file if i have the .itp file alone? I thought i should be able to set it up with any arbitrary coordinates given to the atoms, but LINCS algorithm crahses in restraining the distances. Thanks again Sowmi >Message: 4 >Subject: Re: [gmx-users] tip5p water > From: David >To: gmx-users@gromacs.org >Date: 28 Mar 2003 07:41:08 +0100 >Reply-To: gmx-users@gromacs.org > > >--=-tBvb+ippROYSEua5fl63 >Content-Type: text/plain >Content-Transfer-Encoding: 7bit > >On Fri, 2003-03-28 at 06:47, sowmianarayanan r wrote: > > > > Hi, > > > > I wanted to use TIP5P water model in an ionic solution >simulation > > the model dependence of my systems. I udnerstand that this >water > > model has already been added to Gromacs, but have not been to >find > > the itp file. Can anyone please help me find the tip5p.itp >file? > > > > Thanks > > Sowmi > > > > > > >_______________________________________________________________________ > > Odomos - the only mosquito protection outside 4 walls - > > Click here to know more! > > >http://r.rediff.com/r?http://clients.rediff.com/odomos/Odomos.htm&&odomos&&wn > > > > _______________________________________________ > > gmx-users mailing list > > gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use >the > > www interface or send it to gmx-users-request@gromacs.org. >-- >Groeten, David. >________________________________________________________________________ >Dr. David van der Spoel, Dept. of Cell and Molecular Biology >Husargatan 3, Box 596, 75124 Uppsala, Sweden >phone: 46 18 471 4205 fax: 46 18 511 755 >spoel@xray.bmc.uu.se spoel@gromacs.org >http://xray.bmc.uu.se/~spoel >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >--=-tBvb+ippROYSEua5fl63 >Content-Disposition: attachment; filename=tip5p.itp >Content-Transfer-Encoding: quoted-printable >Content-Type: text/plain; name=tip5p.itp; charset=ISO-8859-1 > >[ defaults ] >; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >1 3 yes 0.5 0.5 > >[ atomtypes ] >;name mass charge ptype sigma epsilon > OW 15.99940 0.000 A 3.12e-01 >6.6944e-01 > HW 1.00800 0.000 A 0.00000E+00 >0.00000E+00 > OL 0.000 -0.241 D 0.00000E+00 >0.00000E+00 > >[ moleculetype ] >; molname nrexcl >SOL 1 > >#define MNO >#ifdef MNO >; We use a strange order of atoms to make things go faster in >GROMACS >[ atoms ] >; id at type res nr residu name at name cg nr charge >1 HW 1 SOL HW1 1 0.241 >2 HW 1 SOL HW2 1 0.241 >3 OL 1 SOL OL1 1 -0.241 >4 OL 1 SOL OL2 1 -0.241 >5 OW 1 SOL OW 1 0 > >[ constraints ] >; i j funct distance >1 5 1 0.09572=20 >2 5 1 0.09572=20 >1 2 1 0.15139 > >[ dummies3 ] >; The position of the dummy is computed as follows: >; >; The distance from OW to OL is 0.07 nm, the geometry is >tetrahedral >; (109.47 deg) >; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 >| >; c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | >; =20 >; >; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) >; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) >; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) > >; Dummy from funct a b c >4 5 1 2 4 -0.344908 -0.344908 >-6.4437903493 >3 5 1 2 4 -0.344908 -0.344908 >6.4437903493 > >[ exclusions ] >1 2 3 4 5 >2 1 3 4 5 >3 1 2 4 5 >4 1 2 3 5 >5 1 2 3 4 > >#else > >[ atoms ] >; id at type res nr residu name at name cg nr charge >1 OW 1 SOL OW 1 0 >2 HW 1 SOL HW1 1 0.241 >3 HW 1 SOL HW2 1 0.241 >4 OL 1 SOL OL1 1 -0.241 >5 OL 1 SOL OL2 1 -0.241 > >[ settles ] >; i funct doh dhh >1 1 0.09572 0.15139 > >[ dummies3 ] >; The position of the dummy is computed as follows: >; >; The distance from OW to OL is 0.07 nm, the geometry is >tetrahedral >; (109.47 deg) >; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 >| >; c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | >; =20 >; >; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) >; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) >; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) > >; Dummy from funct a b c >4 1 2 3 4 -0.344908 -0.344908 >-6.4437903493 >5 1 2 3 4 -0.344908 -0.344908 >6.4437903493 > >[ exclusions ] >1 2 3 4 5 >2 1 3 4 5 >3 1 2 4 5 >4 1 2 3 5 >5 1 2 3 4 >#endif > >--=-tBvb+ippROYSEua5fl63-- _______________________________________________________________________ Odomos - the only mosquito protection outside 4 walls - Click here to know more! http://r.rediff.com/r?http://clients.rediff.com/odomos/Odomos.htm&&odomos&&wn