[gmx-users] angle constraints

[Mark Abraham]

On 24/07/2012 6:07 PM, Broadbent, Richard wrote:
> An Angle constraint amounts to fixing a triangle. To do this you need to
> constrain the distances between all the atoms as you know the of the bonds
> 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
> trivial geometry problem calculate the length of the third side of the
> triangle (6064,6065). However, as you are attempting to hold these atoms in
> a straight line I would suggest that a type 2 virtual site might (depending
> on your system) be a better idea.

Indeed, a much better idea.

Mark

>
> Richard
>
>
> On 24/07/2012 07:21, "tarak karmakar" <tarak20489 at gmail.com> wrote:
>
>> Oh ! Thnaks
>> I saw that table, the angle_restrain option is there but not constraints .
>> Anyway if suppose, I fix the distance between the two terminal atoms
>> of the molecule, the angle will eventually be fixed at a particular
>> given value. Is that the logic ?
>> Actually I searched for this problem so many times but didn't get
>> proper clue; in one of those mails I saw someone has dealt with some
>> dummy atoms. I could not able to digest that logic.
>>
>> On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>> wrote:
>>> On 24/07/2012 3:21 PM, tarak karmakar wrote:
>>>> Dear All,
>>>>
>>>>
>>>> I am constraining one angle in my protein sample by incorporating " [
>>>> constraints ]" block in topology file as
>>>>
>>>>
>>>> [ constraints ]
>>>> ;  index1  index2  index3   funct     angle
>>>>    6064 6063 6065     1   180.0
>>>>
>>>> while doing that its showing the following error
>>>>
>>>> Program grompp, VERSION 4.5.5
>>>> Source code file: topdirs.c, line: 174
>>>>
>>>> Fatal error:
>>>> Invalid constraints type 6065
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> As you will see in table 5.6, this is not a valid option for [constraints] -
>>> you can only specify bonds. You will need to construct a triangle of bond
>>> constraints.
>>>
>>> Mark
>>>
>>>
>>>>
>>>> Then I rechecked the angle block, that specific angle is there in that
>>>> angle section, part of it as follows
>>>>    6039  6057  6058     1
>>>>    6039  6057  6059     1
>>>>    6058  6057  6059     1
>>>>    6064  6063  6065     1
>>>>    6067  6066  6068     1
>>>>    6067  6066  6069     1
>>>>    6068  6066  6069     1
>>>>    6071  6070  6072     1
>>>>    6071  6070  6073     1
>>>>    6072  6070  6073     1
>>>>
>>>> [ constraints ]
>>>> ;  index1  index2  index3   funct     angle
>>>>    6064 6063 6065     1   180.0
>>>>
>>>> [ dihedrals ]
>>>> ;  ai    aj    ak    al funct            c0            c1
>>>> c2            c3            c4
>>>>
>>>>
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