[gmx-users] using dummy atoms

[David van der Spoel]

vips g wrote:
> dear gmx-users
>             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 nrexcl
> HYD            2
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> #ifdef _FF_OPLS
> 1 opls_966 1    HYD   H1     1     0.475
> 2 opls_967 1    HYD   H2     1     0.475
> 3 opls_968 1    HYD   DH    1    -0.950
> #endif
> 
> [dummies2]
> ;Dummy from from funct    a
>    3         1        2     1      0.07
> will this file work for me.
you probably want 0.5 iso 0.07


> can any1 suggest me about this problem.
> Thanks
> Vipul
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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