[gmx-users] distance_restraints with flexible angle

[tarak karmakar]

Exactly so. But in the ffbonded.itp file there are two columns,
equilibrium bond length and Kb . So evenif I give zero then it won't
affect the bond .
Thanks a lot for the reply, it's working fine now .
On Mon, Jul 23, 2012 at 6:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/23/12 8:31 AM, tarak karmakar wrote:
>>
>> Thanks for the reply.
>> But then what should I give as Kb [ bond stretching constant ] in the
>> ffbonded.itp file ? should I give 00.000 there or something else ???
>>
>
> Constraints make bonds rigid.  The force constant is irrelevant.
>
> -Justin
>
>
>> On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 7/23/12 2:39 AM, tarak karmakar wrote:
>>>>
>>>>
>>>> Dear All,
>>>>
>>>>
>>>>     In my simulation I want to fix the S=O bond length of SO2, but the
>>>> angle has to be kept flexible. So I search for the distance restraints
>>>> in gromacs mailing list and
>>>> accordingly I have incorporated the distant_restraints block in the
>>>> topology file. After a short equilibration, when I am seeing the movie
>>>> of the trajectory, the bond length is changing. So what is the right
>>>> way to keep the distance fixed and the angle flexible ?
>>>
>>>
>>>
>>> Use constraints for the bonds, not distance restraints.
>>>
>>> -Justin
>>>
>>>
>>>>      Part of the topology file is as follows
>>>>
>>>>
>>>> ; Include forcefield parameters
>>>> #include "./amber94ff/forcefield.itp"
>>>>
>>>> [ moleculetype ]
>>>> ; Name            nrexcl
>>>> Other_chain_A       3
>>>>
>>>> [ atoms ]
>>>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>>>> typeB    chargeB      massB
>>>> ; residue 502 SR  rtp CR   q  0.0
>>>>        1         S    502     SR      S      1     0.6512      32.07  ;
>>>> qtot 0.6512
>>>>        2         O    502     SR    O1      2    -0.3256         16   ;
>>>> qtot 0.3256
>>>>        3         O    502     SR    O2      3    -0.3256         16   ;
>>>> qtot 0
>>>>
>>>> [ bonds ]
>>>> ;  ai    aj funct            c0            c1            c2
>>>> c3
>>>>       1     2     1
>>>>       1     3     1
>>>>
>>>> [ distance_restraints ]
>>>> ;  ai    aj type index type' low up1 up2 fac
>>>>      1     2     1     0      1   1.149  1.490  1.490  1.0
>>>>      1     3     1     0      1   1.149  1.490  1.490  1.0
>>>>
>>>> [ angles ]
>>>> ;  ai    aj    ak funct            c0            c1            c2
>>>> c3
>>>>       2     1     3     1
>>>>
>>>> ; Include Position restraint file
>>>> #ifdef POSRES
>>>> #include "posre.itp"
>>>> #endif
>>>>
>>>> ; Include water topology
>>>> #include "./amber94.ff/spc.itp"
>>>>
>>>> #ifdef POSRES_WATER
>>>> ; Position restraint for each water oxygen
>>>> [ position_restraints ]
>>>> ;  i funct       fcx        fcy        fcz
>>>>      1    1       1000       1000       1000
>>>> #endif
>>>>
>>>> ; Include topology for ions
>>>> #include "./amber94.ff/ions.itp"
>>>>
>>>> [ system ]
>>>> ; Name
>>>> Protein in water
>>>>
>>>> [ molecules ]
>>>> ; Compound        #mols
>>>> Other_chain_A       1
>>>> SOL               622
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>>
>>> --
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>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> --
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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