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-requ...@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.abra...@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"<tarak20...@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.abra...@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
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