[gmx-users] How to control 1-5 interaction
David van der Spoel
spoel at xray.bmc.uu.se
Thu Mar 18 09:02:01 CET 2004
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.
> / \
> CH3 C----
> atom i ||
> 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
> 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
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 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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