[gmx-users] Position restraint and distance restraints

[jayant james]

*hi!
I am attempting to run a distance & position restrained simulation in water.
The **distance and position restraining files are called from the *.top file
as posres.itp and disres.itp. After a 200ps run I do not see the distance
nor position restraining kicking in. I am not sure if I have specified every
thing correctly. I have pasted essential parts of the topology file, em.mdp,
pr.mdp, disres.itp and posres.itp. Awaiting your feedback
Thanks
Jayant James
*
*TOP FILE*

; Include Position restraint file
#ifdef POSRES
;include "posre.itp"
#endif

;include"disres.itp"

; Include water topology
#include "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 generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein_D           1
SOL         70360
NA+         14


*em.mdp

*;
;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE -DPOSRES
constraints         =  none
integrator          =  steep
nsteps              =  100000
disre               =  simple
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

*pr.mdp*

title               =  Nterm of TnC free (1-19) and TnT fully constrained
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES -DFLEXIBLE
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  100000   ; total 200 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  5000
nstlog              =  5000
nstenergy           =  5000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
disres              =  simple
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein     Non-Protein
tau_t               =  0.1         0.1
ref_t               =  300         300
; Energy monitoring
energygrps          =  Protein     Non-Protein
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

*disres.itp

*[ distance_restraints ]*
*;       ai      aj      type    index   type'   low     up1     up2     fac
        973     926     1       1       1       20.7    21.7    30.5    1.0
        842     926     1       1       1       16.3    17.3    20.9    1.0
        429     926     1       1       1       40.15   41.15   52.85   1.0
        973     1079    1       1       1       39.45   30.45   48.75   1.0
        842     1079    1       1       1       21.85   22.85   33.55   1.0
        429     1079    1       1       1       40      42      65.3    1.0
        973     1148    1       1       1       38      39      61.2    1.0
        842     1148    1       1       1       32      33.75   53.7    1.0
        429     1148    1       1       1       52      54.9    72.9    1.0
        973     1216    1       1       1       42      46.35   69.25   1.0
        842     1216    1       1       1       43      43.85   64.55   1.0
        429     1216    1       1       1       57      59.8    81.6    1.0
        973     1284    1       1       1       48      50.05   76.35   1.0
        842     1284    1       1       1       45      47.4    76.9    1.0
        429     1284    1       1       1       55      58.95   94.45   1.0
*
posres.itp*

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1  1000  1000  1000
     5     1  1000  1000  1000
     6     1  1000  1000  1000
     7     1  1000  1000  1000
     8     1  1000  1000  1000
     9     1  1000  1000  1000
    10     1  1000  1000  1000
    11     1  1000  1000  1000
    12     1  1000  1000  1000
    14     1  1000  1000  1000
    15     1  1000  1000  1000
.   .
.   .
.   .
.   .
.   .
.   .




-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
Residence -24935864, cell-9841042164
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