[gmx-users] distance_restraints with flexible angle

[Justin Lemkul]

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

========================================