[gmx-users] distance restraint

[Mark Abraham]

Pathumwadee Intharathep wrote:
> 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

This is probably a bad idea... see 
http://wiki.gromacs.org/index.php/Thermostats

> 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?

It's a label for the individual restraints, in case you need to refer to 
them. Guessing wildly, I suppose you might need labels to create sets 
for NMR time-averaged distance restraints.

> Q2:Where can I find in the output to make sure that my distances has 
> already restrainted?

The energy contributions from the restraints will be listed in the .log 
and the .edr files.

Mark