[gmx-users] distance restraint

[Pathumwadee Intharathep]

Dear gmx's user,
May I asked you some technicl Questions?
Do you know how to make distance restraint in gromacs?
what I did I have created file name "disre.itp" as shown below
[ distance_restraints ]
;   ai    aj     type index type low up1 up2 fac
   489   1133   1   1     1   0.25 0.35 0.40 1.0
   489   1164   1   2     1   0.25 0.35 0.40 1.0
   490   1127   1   3     1   0.25 0.35 0.40 1.0
   490   1167   1   4     1   0.25 0.35 0.40 1.0
 
in md.mdp file:
 
title               = M2_amand in POPC
cpp                 =  /lib/cpp
constraints         =  all-bonds
define              =  -DDISRES
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  500000   ; total 1000 ps = 1 ns !
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.2
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  POPC SOL  Cl
tau_t               =  0.1      0.1  0.1  0.1
ref_t               =  310      310  310  310
; Energy monitoring
energygrps          =  Protein  POPC  SOL  Cl
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  310.0
disres              =  simple


in topology.top file I added...

; Include distance restraint file
#ifdef DISRES
#include "disre.itp"
#endif

My questions are 
Q1:What is "column index" mean in disre.itp file? and how is it benefit?
Q2:Where can I find in the output to make sure that my distances has already restrainted?

 Thanks so much
 
pathum



      
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