[gmx-users] to David Mobley, question about angle restraints

David Mobley dmobley at gmail.com
Sat Nov 12 21:49:16 CET 2005


Responses below.

> 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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