[gmx-users] positional restraint

[Alok]

hello gmx uers,
                        I have a problem concerning positional restraint 
. I am constraining a residue from my protein during minimization and 
consequently during the early  stage of my dynamics. I have consequently 
constructed an ".itp file" for the purpose of positional restraint of 
the residue which i then add to the ".top file".

The  .itp file is as shown below:

; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type      fx      fy      fz
   691     1      100000  100000  100000
   692     1      100000  100000  100000
   693     1      100000  100000  100000
   694     1      100000  100000  100000
   695     1      100000  100000  100000
   696     1      100000  100000  100000
   697     1      100000  100000  100000
   698     1      100000  100000  100000
   699     1      100000  100000  100000
   700     1      100000  100000  100000
   701     1      100000  100000  100000

The output data that i get after preprocessing my input files for 
minimization is as follows:

processing coordinates...
double-checking input for internal consistency...
Reading position restraint coords from out2sxl.gro
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   39330
#   G96BONDS:   2817
#     ANGLES:   26220
#  G96ANGLES:   5464
#      PDIHS:   2470
#      IDIHS:   2285
#       LJ14:   4581
#     POSRES:   22

Here i observe that the POSRES: 22 value is twice the number of atoms 
 of the residue (11 atoms) I want to constrain.

Also the values reported for the other terms like BONDS,ANGLES, etc 
looks not to tally with the actual number present in the system.

I tried preprocessing the input files with different number of atoms in 
the ".itp file" but everytime the POSRES value is twice the actual 
number of atoms.
 
Can anyone please tell me the reason for this ???????

Also i would like to mention that if i still run the Mdrun program i get 
the position restraint energy term in my energy list output file which 
suggest that my constrain in functioning.Still I am confused about the 
number of atoms reported for constraining after preprocessing.
                                                                        
                                                                        
                                        Thanking you,
                                                                        
                                                                        
                                             Alok jain