http://www.sklogwiki.org/SklogWiki/api.php?action=feedcontributions&feedformat=atom&user=129.215.4.47 2026-05-01T00:05:15Z User contributions MediaWiki 1.41.0 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20494 2021-05-25T14:26:12Z

<p>129.215.4.47: </p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458 <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20493 2021-05-25T14:25:12Z

<p>129.215.4.47: made the top.top into a code by adding a &#039; &#039; at start of every line</p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> <br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458 <br /> <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20492 2021-05-25T14:23:46Z

<p>129.215.4.47: </p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> '''The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top'''<br /> <br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> <br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458 <br /> <br /> <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> ;<br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20491 2021-05-25T14:22:17Z

<p>129.215.4.47: </p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> '''The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top'''<br /> <br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> <br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> <br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458<br /> <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> ;<br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20490 2021-05-25T14:21:38Z

<p>129.215.4.47: </p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> '''The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top'''<br /> <br /> ;<br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> <br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> <br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458<br /> <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> ;<br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47 http://www.sklogwiki.org/SklogWiki/index.php?title=GROMACS_topology_file_for_the_TIP4P/Ice_model&diff=20489 2021-05-25T14:21:12Z

<p>129.215.4.47: </p> <hr /> <div>The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. <br /> <br /> '''The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top'''<br /> <br /> ```<br /> <br /> [ defaults ]<br /> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br /> 1 2 no 1.0 1.0<br /> <br /> [atomtypes]<br /> ;name mass charge ptype sigma epsilon<br /> IW 0 0.000 D 0.0 0.0<br /> OWT4 15.99940 0.000 A 0.31668 0.88211<br /> HW 1.00800 0.000 A 0.00000E+00 0.00000E+00<br /> <br /> <br /> [moleculetype]<br /> ; name nrexcl<br /> water 1<br /> <br /> [atoms]<br /> ; nr type resnr residu atom cgnr charge<br /> 1 OWT4 1 water OW1 1 0 15.994<br /> 2 HW 1 water HW2 1 0.5897 1.008<br /> 3 HW 1 water HW3 1 0.5897 1.008<br /> 4 IW 1 water MW4 1 -1.1794 0.0<br /> <br /> [constraints]<br /> ;i j funct doh dhh<br /> 1 2 1 0.09572<br /> 1 3 1 0.09572<br /> 2 3 1 0.15139<br /> <br /> [exclusions]<br /> 1 2 3 4<br /> 2 1 3 4<br /> 3 1 2 4<br /> 4 1 2 3<br /> <br /> <br /> <br /> ; The position of the dummy is computed as follows:<br /> ;<br /> ; O<br /> ;<br /> ; D<br /> ;<br /> ; H H<br /> ;<br /> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br /> ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]<br /> <br /> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)<br /> <br /> <br /> [dummies3]<br /> ; Dummy from funct a b<br /> 4 1 2 3 1 0.13458 0.13458<br /> <br /> <br /> [system]<br /> water TIP4P/Ice<br /> <br /> [molecules]<br /> water 1<br /> <br /> <br /> ```<br /> <br /> [[category: models]]<br /> [[category: water]]</div>

129.215.4.47