[gmx-users] How to control 1-5 interaction

[David van der Spoel]

On Thu, 2004-03-18 at 08:15, Makoto Yoneya wrote:
> Dear GROMACS users:
> 
> I'd like to know the proper way to control 1-5 interaction within molecule.
> The 1-5 interaction which I'd like to control is as following.
> 
>         \
>          CH2
>            \
>        H--C---O
>           /        \
>         CH3      C----
>       atom i     ||
>                    O
>                atom j
> 
> Between the branched CH3 (i) and the carbonyl O (j) , there is rather strong
> interaction even that is 1-5 distance.
> A possible way will be as follows.
> 
> [ exclusions ]
>   i    j
>   j    i
> [ pairs ]
>   i    j     1    0.****E-02   0.****E-05  ; control this interaction
> parameters
> 
> Is this correct way to control the 1-5 interaction?
> Are there more adequate way?

This will work. The disadvantage is that you have to list the
interactions yourself. As an alternative you can increase the number of
exclusions in a molecule:
[ moleculetype ]
; Name	nrexcl
MyMOL	4

then, if you do want interactions, you still need to add them manually,
in the pairs sections.
> 
> Thank you for advance.
> 
> Makoto Yoneya Dr.
> Yokoyama Nano-structured LC Project
> Tsukuba, Japan
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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