[gmx-users] distance_restraints with flexible angle

[tarak karmakar]

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 ???

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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-- 
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