[gmx-users] using dummy atoms

Sat Apr 5 18:48:51 CEST 2008

dear gmx-users&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I want to simuate the hydrogen gas as a three point molecule with two hydrogen atoms and a dummy atom placed at their midpoint. the charge on the h atoms is 0.475 and that on dummy atom is -0.950.I am trying to make a "hydrogen.itp" file. [ moleculetype ]; molname nrexclHYD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2[ atoms ]; nr type resnr residue atom cgnr charge mass#ifdef _FF_OPLS 1 opls_966&nbsp;1&nbsp;&nbsp;&nbsp; HYD&nbsp;&nbsp; H1&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp; &nbsp;0.4752 opls_967 1&nbsp;&nbsp; &nbsp;HYD&nbsp;&nbsp; H2&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; 0.4753 opls_968 1&nbsp;&nbsp;&nbsp; HYD&nbsp;&nbsp; DH&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp; -0.950#endif[dummies2];Dummy from from funct&nbsp;&nbsp; &nbsp;a&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbs
 p; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.07will this file work for me.can any1 suggest me about this problem.Thanks Vipul
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