[gmx-users] angle constraints

tarak karmakar tarak20489 at gmail.com
Tue Jul 24 11:20:49 CEST 2012

```Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 degree. So what is
the best way of  constraining the angle for the linear molecule ?

On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
>>>>> 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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>>>
>
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--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809

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