[gmx-users] how to constrain a dihedral

[David van der Spoel]

On Wed, 2004-12-08 at 11:17 +0800, mengyi wrote:
> Hi all
> there are two question:
> (1) i want to constrain some dihedrals during MD, 
> such as
>   1     4
>    \    /
>    2---3
> i want keep [1 2 3 4] planar, how can i do it?
If you want to have them analytically planar you have to use dummies. If
a restraint is enough useimproper dihedrals (chpater 4)
> 
> (2) when i use constraints=h-angles, algorithm=shake, it always crash.
>  but if i use constraints=h-bonds there is no problem. why? is there something
> need to do before using angle-constraint?
I assume you mean mdrun crashes? It shouldn't, but check time step.

> 
> thanking you all in advance
> 
> 
> 
> 
> 
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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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