[gmx-users] nmr distance restraints

[Eiso AB]

Hi,
I've setup an mdrun with [ distance restraints ] but the restraints don't
seem to have any effect on the simulation, so I'm wondering if there's
anything i need to do to switch them on that I missed.

gmx disre or gmx nmr doesn't give any info about restraints.
and the .log file doesn't show any energy component for Distance
Restraints, e.g.

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
    4.14550e+03    1.13252e+04    1.29502e+04    9.20032e+01    6.00131e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    5.01723e+03    6.08476e+04    3.13964e+05   -2.12124e+06    5.15532e+03
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -1.70714e+06    2.85181e+05   -1.42196e+06   -1.34064e+06    2.99828e+02
 Pressure (bar)   Constr. rmsd
    1.15517e+02    4.10744e-06

I have defined restraints between protein, ligand and a few waters - all in
different [molecules]
- so I used [ intemolecular_interactions ] followed by [ distance
restraints ]


my topol.top ends like this :

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
lig                 1
SOL         35926
NA               4

[ intermolecular_interactions ]

[ distance_restraints ]
; ai  aj  type index type' low    up1    up2    fac ; # source
  465 564   1  0   1   0.2540 0.2540 0.4115 1  ; # 308 ile hd+ 216 val hg1+
2.54
  465 565   1  0   1   0.2540 0.2540 0.4115 1  ; #
  465 566   1  0   1   0.2540 0.2540 0.4115 1  ; #
  466 564   1  0   1   0.2540 0.2540 0.4115 1  ; #
  466 565   1  0   1   0.2540 0.2540 0.4115 1  ; #
  466 566   1  0   1   0.2540 0.2540 0.4115 1  ; #
  467 564   1  0   1   0.2540 0.2540 0.4115 1  ; #
  467 565   1  0   1   0.2540 0.2540 0.4115 1  ; #
  467 566   1  0   1   0.2540 0.2540 0.4115 1  ; #
[...snap...]
 1607  5241  1 34  1 0.5680 0.5680 0.6384 1  ; # 170 leu hd1# 411 lig h09
5.68
 1608  5241  1 34  1 0.5680 0.5680 0.6384 1  ; #
 1609  5241  1 34  1 0.5680 0.5680 0.6384 1  ; #
[ ..snap ... ]
 2720  5571  1 52  2 0.1900 0.1900 0.2900 1  ; # 217 asp od1 501 sol hw2
1.90
 2720  5569  1 53  2 0.3000 0.3000 0.4000 1  ; # 217 asp od1 501 sol ow
3.00


disre is set to simple. From the mdout.mdp

[]$ grep disre mdout.mdp

; Distance restraints type: No, Simple or Ensemble
disre                    = Simple
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting          = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
; Output frequency for pair distances to energy file
nstdisreout              = 100


gmx dump shows that the run topology has the distance restraints and looks
ok to me

gmx dump -s md_0_10.tpr |grep -10 dis

[..snap..]
Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision)
Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision)
   disre                          = Simple
   disre-weighting                = Conservative
   disre-mixed                    = false
   nstdisreout                    = 100
         0 type=1038 (DISRES) 464 563
         1 type=1038 (DISRES) 464 564
         2 type=1038 (DISRES) 464 565
         3 type=1038 (DISRES) 465 563
         4 type=1038 (DISRES) 465 564
         5 type=1038 (DISRES) 465 565
   [..snap ...]
  D.R.Viol. (nm):
      nr: 0
         [...snap...]

         functype[1038]=DISRES, label=   0, type=1, low= 2.54000008e-01,
up1= 2.54000008e-01, up2= 4.11500007e-01, fac= 1.00000000e+00)
         functype[1039]=DISRES, label=   1, type=1, low= 2.56999999e-01,
up1= 2.56999999e-01, up2= 4.12600011e-01, fac= 1.00000000e+00)
         functype[1040]=DISRES, label=   2, type=1, low= 3.72999996e-01,
up1= 3.72999996e-01, up2= 4.80199993e-01, fac= 1.00000000e+00)
         functype[1041]=DISRES, label=   3, type=1, low= 3.84000003e-01,
up1= 3.84000003e-01, up2= 4.88200009e-01, fac= 1.00000000e+00)
         functype[1042]=DISRES, label=   4, type=1, low= 2.33999997e-01,
up1= 2.33999997e-01, up2= 4.04900014e-01, fac= 1.00000000e+00)
         functype[1043]=DISRES, label=   5, type=1, low= 2.39999995e-01,
up1= 2.39999995e-01, up2= 4.06699985e-01, fac= 1.00000000e+00)
         functype[1044]=DISRES, label=   6, type=1, low= 3.03000003e-01,
up1= 3.03000003e-01, up2= 4.35000002e-01, fac= 1.00000000e+00)

etc...

Any suggestions about what is wrong here would be appreciated
Thanks,

Eiso