[gmx-users] Re: angle constraints

[Thomas Schlesier]

As others said:
type 2 virtual site
check chapter 4.7 and 5.2.2 in the manual (version 4.5.x).

Greetings
Thomas


Am 24.07.2012 12:00, schrieb gmx-users-request at gromacs.org:
> 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
>>>>>> >>>>>For more information and tips for troubleshooting, please check the
>>>>>> >>>>>GROMACS
>>>>>> >>>>>website athttp://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