[gmx-users] to David Mobley, question about angle restraints
dmobley at gmail.com
Sat Nov 12 21:49:16 CET 2005
> I decided to restrain 2 simple angles (ABC) in my system. At the bottom of topology file I wrote:
> [ angle_restraints ]
> ; ai aj ak al type angle force
> 717 3180 3180 3177 1 123 1000
> 2032 3180 3180 3177 1 103 1000
> However, when I obtained tpr file by grompp, it made 4 warnings:
> For the first angle
> 1) Duplicate atom index (3180) in angle_restraints
> As far as I understood, this is normal, as I want to restrain an angle ABC and not ABCD
This is normal. But see my recent correspondence with David van der
Spoel on this list; it turns out that angle restraints for ABBC are
different from angle restraints for ABCB because the cosine of the
angle is computed using a dot product of vectors AB-BC or AB-CB; the
resulting dot product is different by a sign depending on the order.
So make sure you're using the one you want to actually restrain.
> 2) No default Angle Rest. types, using zeroes
> And the same 2 warnings for the second angle.
The format documented in the manual is this:
ai aj ak al type angle force constant multiplicity
1393 1391 1391 2608 1 81 1000 1
It looks like you are missing the multiplicity. I would try adding that.
> What did I do wrong in warning 2?
> Sincerely yours,
> Misha Ivanov
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