[gmx-users] angle constraints

[Broadbent, Richard]

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.

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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>