[gmx-users] Distance restraints

[tarak karmakar]

Dear All,
I'm trying to keep distance restraints between few atoms, and for that I
have done the following,
In the topology file, I have inserted a block specifying the details of
pairs

------------------------------------------------------------------------------------------
; Include forcefield parameters
#include "./amber99sb-ildn.ff/forcefield.itp"

; Include chain topologies
#include "Protein_chain_A.itp"
#ifdef DISRES
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
  3722 3760 1    0     1     0.19 0.22 0.23 1.0
  3722 3765 1    1     1     0.19 0.22 0.23 4.184
  3723 3759 1    2     1     0.19 0.22 0.23 1.0
  3723 3766 1    2     1     0.19 0.22 0.23 1.0
#endif

#include "Protein_chain_B.itp"

; Include water topology
#include "./amber99sb-ildn.ff/tip3p.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 "./amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
SOL         24565
NA               2
-------------------------------------------------------------------
Next in the npt.mdp file I have used the following keywords,
define                  = -DDISRES
disre                   = simple
disre_fc                = 1000

Now, while running the simulations, after few ps the distances are
increasing by 2-3 Ang. Could anyone please suggest me something related to
this?
I went through an old discussion related to the same issue here,
http://comments.gmane.org/gmane.science.biology.gromacs.user/51387

Thanks and regards,
Tarak