[gmx-users] LINCS WARNING "max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000"

[SUN, Jian]

Dear all,

I am running the simulated annealing for a protein solvented in a water box,
but I get such LINCS WARNING as "max 2022834176.000000 (between atoms 5655
and 5658) rms 81089176.000000"
Why? Does it mean that my system is exploring?

The following is my mdp file and some of the LINCS WARNING message:

dt                       = 0.001
; SIMULATED ANNEALING
annealing                = single
annealing_npoints        = 3
annealing_time           = 0 50 800
annealing_temp           = 0 350 0

gen_vel                  = no
gen_temp                 = 0
gen_seed                 = 173529
constraints              = all-bonds


constraint_algorithm     = lincs
lincs_order              = 4
lincs_iter               = 2


Step 263643, time 263.643 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    190    192   32.5    0.1336   0.1773      0.1335
    192    193   47.2    0.1011   0.1537      0.1010
.......
   5643   5646  151.3  2714.9613 68555.9304      0.1529
   5646   5647   65.9  1894.6184 216204.0509      0.1090
   5646   5648   69.8  1818.5108 212516.4615      0.1090
   5649   5650  173.5  447425.3856 22302675.1767      0.1229
   5649   5651  156.8  1680664.1544 50630117.0698      0.1335
   5651   5652  146.9  1789339.4529 46335793.8246      0.1010
   5651   5653  174.1  5949343.3105 149770966.9350      0.1449
   5653   5654  171.6  7324940.0095 183521837.1456      0.1090
   5653   5655  177.6  16072804.7240 243272781.1728      0.1529
   5653   5669  178.4  5469409.9743 152675417.1142      0.1522
   5655   5656  177.8  18428095.3131 204639707.3293      0.1090
   5655   5657  176.6  18485738.1080 204477063.8333      0.1090
   5655   5658  179.1  30390583.4845 305447945.4836      0.1510
   5658   5659  179.2  30123192.5220 273034063.5045      0.1400
   5658   5661  178.6  29490165.1653 271759183.7457      0.1400
   5659   5660  176.4  17471940.7463 154679010.3056      0.1080
   5659   5663  178.5  16208110.3050 148729415.1683      0.1400
   5661   5662  177.2  16669061.9731 152805630.9454      0.1080
   5661   5665  177.7  14573623.8544 146053907.4077      0.1400
   5663   5664  177.0  9332011.5148 90334896.9046      0.1080
   5663   5667  176.5  9190421.7390 97130164.6485      0.1400
   5665   5666  175.0  8010325.5108 87779001.5722      0.1080
......
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