[gmx-users] distance_restraints with flexible angle

[Justin Lemkul]

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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