[gmx-users] exclusions indices

[David van der Spoel]

On Thu, 2005-05-12 at 16:22 +0800, xieyh at hkusua.hku.hk wrote:
> Dear users:
> 
> In my system, 2 molecules and solvent (protein DNA SOL) are contained. Now, I
> expect to exclude the nonbonded interactions between e.g. atoms 1, 2 ,3 4 in
> DNA and all the atoms in SOL. 
> 
> Normally, I can realize it by defining a [ exclusions ] section. But in my case,
> the number for SOL is huge, so it is almost impossible to explicitly write each
> SOL atom number while defining [ exclusions ]. Can you suggest any simple one,
> it has better be like:
> 
> [ exclusions ]
> 1   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
> 2   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
> 3   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
> 4   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
> 
> I think GMX can do it, but how?
energy_excl in the mdp file
> 
> 
> Thanks and regards,
> Xie YH 
> Hong Kong Univ.
> 
> 
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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://xray.bmc.uu.se/~spoel
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