How to choose the positions of the dummy atoms while constraining the
angle for a linear triatomic molecule?
The topology for a such molecule ( af for example CO2 ) is as follows
[ moleculetype ]
; Name nrexcl
CO2 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 503 CO rtp CO q 0.0
1 D1 503 CO D1 1 0 21.90158
; qtot 0
2 D2 503 CO D2 2 0 21.90158
; qtot 0
3 CE 503 CO CO 3 0.7 0.00000
; qtot 0.7
4 OE 503 CO OC1 4 -0.35 0.00000
; qtot 0.35
5 OE 503 CO OC2 5 -0.35 0.00000
; qtot 0.35
[ constraints ]
; ai aj funct b0
1 2 1 0.2000
[ dummies2 ]
; ai aj ak funct a
3 1 2 1 0.0170
4 1 2 1 0.1000
5 1 2 1 0.2170
[ exclusions ]
3 4 5
4 5 3
5 4 3
The .rtp file for CO2
[ CO ]
[ atoms ]
D1 D1 0.0000 1
D2 D2 0.0000 2
CO CE 0.7000 3
OC1 OE -0.3500 4
OC2 OE -0.3500 5
[ bonds ]
CO OC1
CO OC2
Can anyone please check above file parts whether I'm doing correct or not ?
On Tue, Jul 24, 2012 at 4:25 PM, Thomas Schlesier <[email protected]> wrote:
> 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 [email protected]:
>>
>> 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<[email protected]>
>> 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"<[email protected]> 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<[email protected]>
>>>>> >>>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
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>
>>>>>> >>>>--
>>>>>> >>>>gmx-users mailing [email protected]
>>>>>> >>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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--
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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