[Fwd: Re: [gmx-users] dummy atom vdw interactions]

David spoel at xray.bmc.uu.se
Wed Aug 3 09:42:15 CEST 2005

> Subject: Re: [gmx-users] dummy atom vdw interactions
> Date: Wed, 3 Aug 2005 00:05:48 -0700 (PDT)
> You are right, David. For a system of two types of
> atom (one 'real' and one 'dummy', with different sigma
> and epsilon), there are four types of functype.

Do you find four different LJ parameters in the tpr file then?

> However, from the simulation, putting one dummy and
> one real together, there is no replusion. May I know
> where the source code dealing with vdw and dummy is?
Check grompp.c

> Yang Ye

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://xray.bmc.uu.se/~spoel

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