[gmx-users] angle constraint not fixing the length of bonds or angles of the residue

[Javaria ashraf]

hello kind users
I am working on a protein, in which i need to freeze some residue. I have applied freeze group, position restraint and distance restraint options but the residues deviate in energy minimization phase. i have switched to constraint which says "constraint fix the length of bonds or angles". I have explicitly defined the constraint block in * .top file. 
constraint block in .top file
[ constraints ]
;   i     j        ?        up1(nm)     up2(nm)
 1058  1059 2   0.100972   0.100972 
 1059  1060 2   0.213104   0.213104
 1058  1060 2   0.145789   0.145789
 1060  1061 2   0.109028   0.109028
 1060  1062 2   0.154404   0.154404
 1058  1062 2   0.248402   0.248402
 1072  1061 2   0.213016   0.213016
 1072  1062 2   0.249125   0.249125
 1060  1072 2   0.152379   0.152379
 1062  1063 2   0.108979   0.108979
 1064  1068 2   0.251251   0.251251
 1068  1060 2   0.251860   0.251860
 1064  1060 2   0.251554   0.251554
 1062  1064 2   0.153058   0.153058
 1062  1068 2   0.152741   0.152741
 1064  1065 2   0.109001   0.109001 
 1064  1066 2   0.108990   0.108990
 1064  1067 2   0.109026   0.109026
 1068  1069 2   0.109019   0.109019
 1068  1071 2   0.109006   0.109006
....
....
 1062  1069 2   0.215236   0.215236 

When i run the energy minimization step using implicit solvent = GBSA using forcefield oplsaa. The angles current position deviates greatly and generate lincs warning. e.g

.mdp file is attached and there is no error and warning generated in running grommp command but when i run mdrun it gives following lincs warning and unstable structure.
 Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 47.479051, max 104.334671 (between atoms 1062 and 1068)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates

Back Off! I just backed up em-const.trr to ./#em-const.trr.3#

Back Off! I just backed up em-const.edr to ./#em-const.edr.3#

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =         1000

WARNING: Listed nonbonded interaction between particles 1056 and 1062
at distance 4.799 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Step=    0, Dmax= 1.0e-02 nm, Epot=  1.31942e+08 Fmax= 5.25261e+11, atom= 1060
Step 1, time 0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1815.564375, max 4093.398682 (between atoms 1060 and 1072)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1058   1059  171.5    0.5660  70.7067      0.1010
   1059   1060  169.9    1.2350 404.5788      0.2131
   1058   1060  151.2    0.9028 336.9464      0.1458
   1060   1061  151.5    1.0505 334.5118      0.1090
   1058   1062  153.5    4.6714 326.4363      0.2484
   1072   1061  174.8    2.9044 352.7521      0.2130
   1072   1062  159.3    5.4856 456.8948      0.2491
   1060   1072  172.3    3.3869 623.9004      0.1524
   1064   1068   48.2    4.3189 182.9372      0.2513
   1068   1060  168.4    5.6927 520.6365      0.2519
   1064   1060  144.2    4.8385 423.7913      0.2516
   1062   1064  164.2    4.2594 369.4854      0.1531
   1062   1068  145.8    5.9015 345.7090      0.1527
   1064   1065   61.8    4.2437  84.9125      0.1090
   1064   1067   48.7    6.4428  63.1181      0.1090
   1069   1070   42.3    3.6125  18.9214      0.1780
   1070   1062   37.7    4.7731 341.3928      0.2152
   1062   1071   41.4    5.9389 342.8665      0.2152
   1065   1066  106.0    3.4433  14.4106      0.1780
   1065   1067  164.6    3.6088  36.8630      0.1780
   1066   1067  117.0    2.4012  15.7321      0.1779
   1062   1067   62.0    5.8630 327.1110      0.2155
   1065   1062   51.0    4.0083 338.4389      0.2155
   1066   1062   78.9    4.3064 326.0625      0.2155
   1068   1063  175.5    6.0463 248.0030      0.2127
   1060   1063   84.7    0.7192 279.9834      0.2165
   1064   1063  159.4    4.7665 140.1502      0.2154
   1058   1072  173.7    3.1276 366.4720      0.2430
   1072   1073  172.3    2.2672 327.7513      0.1230
   1072   1074  175.2    2.5309 318.4125      0.1327
   1060   1073  177.5    1.5295 399.3600      0.2396
   1074   1073  116.7    0.3793  34.3242      0.2248
   1062   1061  155.8    4.9561 375.3529      0.2156
   1062   1069   69.6    2.9536 318.7583      0.2152

the output structure has much greater distances between two angles e.g if distance between two atoms is 1.0097Angstrom it changes to 12.003Angstrom.
Constraint means to fix the length but its not fixing it. I have searched the mail archive but haven't got any answer. kindly guide me where i am going wrong using constraint.
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