Dear all,<br>
<br>
I am running the simulated annealing for a protein solvented in a water box,<br>
but I get such LINCS WARNING as "max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000"<br>
Why? Does it mean that my system is exploring? <br>
<br>
The following is my mdp file and some of the LINCS WARNING message:<br>
<br>
dt
= 0.001<br>
; SIMULATED ANNEALING<br>
annealing = single<br>
annealing_npoints = 3<br>
annealing_time = 0 50 800<br>
annealing_temp = 0 350 0<br>
<br>
gen_vel = no<br>
gen_temp = 0<br>
gen_seed = 173529<br>
constraints = all-bonds<br>
<br>
constraint_algorithm = lincs<br>
lincs_order = 4<br>
lincs_iter = 2<br>
<br>
<br>
Step 263643, time 263.643 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
190 192
32.5 0.1336
0.1773 0.1335<br>
192 193
47.2 0.1011
0.1537 0.1010<br>
.......<br>
5643 5646 151.3 2714.9613 68555.9304 0.1529<br>
5646 5647 65.9 1894.6184 216204.0509 0.1090<br>
5646 5648 69.8 1818.5108 212516.4615 0.1090<br>
5649 5650 173.5 447425.3856 22302675.1767 0.1229<br>
5649 5651 156.8 1680664.1544 50630117.0698 0.1335<br>
5651 5652 146.9 1789339.4529 46335793.8246 0.1010<br>
5651 5653 174.1 5949343.3105 149770966.9350 0.1449<br>
5653 5654 171.6 7324940.0095 183521837.1456 0.1090<br>
5653 5655 177.6 16072804.7240 243272781.1728 0.1529<br>
5653 5669 178.4 5469409.9743 152675417.1142 0.1522<br>
5655 5656 177.8 18428095.3131 204639707.3293 0.1090<br>
5655 5657 176.6 18485738.1080 204477063.8333 0.1090<br>
5655 5658 179.1 30390583.4845 305447945.4836 0.1510<br>
5658 5659 179.2 30123192.5220 273034063.5045 0.1400<br>
5658 5661 178.6 29490165.1653 271759183.7457 0.1400<br>
5659 5660 176.4 17471940.7463 154679010.3056 0.1080<br>
5659 5663 178.5 16208110.3050 148729415.1683 0.1400<br>
5661 5662 177.2 16669061.9731 152805630.9454 0.1080<br>
5661 5665 177.7 14573623.8544 146053907.4077 0.1400<br>
5663 5664 177.0 9332011.5148 90334896.9046 0.1080<br>
5663 5667 176.5 9190421.7390 97130164.6485 0.1400<br>
5665 5666 175.0 8010325.5108 87779001.5722 0.1080<br>
......<br>