[gmx-users] distance_restraints with flexible angle

[tarak karmakar]

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 ?
   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

-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
JNCASR