[gmx-users] LINCS WARNING: How to correct LINCS WARNINGs
Mr.Sridhar
sridhar at www.cdfd.org.in
Sat May 3 15:40:02 CEST 2003
Dear gmx users,
I was running a MD simulation of a 49 aa protein in spc216 water. I used
the GROMOS96 force field. The .mdp file is attached. The program ran well
for some and then started giving LINCS warnings like "relative constraint
deviation after LINCS:" and " bonds that rotated more than 30 degrees:"
etc. The program got terminated prematurely after some such warnings.
Could anybody explain what these warnings mean and how to overcome them.
Thanking you
sridhar.
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Step 531694, time 1063.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.012529 (between atoms 422 and 423) rms 0.000569
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
422 423 53.3 0.0995 0.1013 0.1000
422 424 47.9 0.1052 0.0999 0.1000
Step 531695, time 1063.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.103722 (between atoms 422 and 424) rms 0.004843
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
422 423 89.9 0.1013 0.1030 0.1000
422 424 90.1 0.0999 0.1104 0.1000
Step 531696, time 1063.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.165007 (between atoms 422 and 423) rms 0.008281
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
422 423 90.0 0.1030 0.1165 0.1000
422 424 90.0 0.1104 0.1081 0.1000
Step 531697, time 1063.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 15.816898 (between atoms 422 and 423) rms 0.708829
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
420 421 41.6 0.1225 0.1365 0.1230
422 423 90.2 0.1165 1.6817 0.1000
422 424 85.4 0.1081 0.0852 0.1000
Constraint error in algorithm Lincs at step 531697
Step 531698, time 1063.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.868689 (between atoms 422 and 424) rms 0.061591
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
420 422 96.9 0.1394 0.2395 0.1330
422 423 70.4 1.6817 0.1540 0.1000
422 424 92.6 0.0852 0.1869 0.1000
Constraint error in algorithm Lincs at step 531698
Step 531699, time 1063.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 12.338169 (between atoms 422 and 423) rms 0.555821
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
418 419 35.3 0.1664 0.1401 0.1530
419 420 37.2 0.1232 0.1575 0.1530
420 421 84.0 0.0752 0.1554 0.1230
420 422 65.5 0.2397 0.2030 0.1330
422 423 89.6 0.1541 1.3338 0.1000
422 424 94.5 0.1870 0.2125 0.1000
Constraint error in algorithm Lincs at step 531699
Step Time Lambda Annealing
531700 1063.40002 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 25.493540 422 423 1.159729
After LINCS 3.092451 422 424 0.149503
Step 531700, time 1063.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 3.092451 (between atoms 422 and 424) rms 0.149503
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
418 419 37.2 0.1394 0.1507 0.1530
420 422 91.4 0.2019 0.2175 0.1330
422 423 90.8 1.3267 0.2066 0.1000
422 424 90.2 0.2113 0.4092 0.1000
Constraint error in algorithm Lincs at step 531700
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.76596e+03 5.06114e+02 5.95908e+02 2.70890e+02 5.18845e+03
LJ (SR) LJ (LR) Coulomb (SR) Potential Kinetic En.
1.95515e+04 -3.79527e+02 -1.42572e+05 -1.15073e+05 1.03516e+05
Total Energy Temperature Pressure (bar)
-1.15569e+04 1.49685e+03 -2.84462e+04
Step 531701, time 1063.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 9.955848 (between atoms 422 and 423) rms 0.465480
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
418 419 30.2 0.1510 0.1715 0.1530
420 421 41.8 0.1066 0.1352 0.1230
420 422 88.6 0.2179 0.1378 0.1330
422 423 89.0 0.2070 1.0956 0.1000
422 424 91.8 0.4099 0.3958 0.1000
Constraint error in algorithm Lincs at step 531701
Step 531702, time 1063.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 4.915229 (between atoms 422 and 424) rms 0.237329
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
416 418 32.5 0.1478 0.1587 0.1470
418 419 46.8 0.1712 0.1680 0.1530
418 425 30.3 0.1537 0.1616 0.1530
419 420 36.6 0.1653 0.1576 0.1530
420 421 32.3 0.1349 0.1347 0.1230
420 422 90.1 0.1376 0.2191 0.1330
422 423 90.1 1.0937 0.2855 0.1000
422 424 90.0 0.3951 0.5915 0.1000
Constraint error in algorithm Lincs at step 531702
Step 531703, time 1063.41 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 67.352615 (between atoms 422 and 423) rms 5.152792
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
399 401 108.2 0.1471 0.4118 0.1470
401 402 99.5 0.1530 0.4215 0.1530
401 414 65.8 0.1536 0.7877 0.1530
414 415 77.1 0.1236 0.7751 0.1230
414 416 137.0 0.1340 2.1632 0.1330
416 417 61.9 0.1005 2.3163 0.1000
416 418 43.7 0.1585 3.0239 0.1470
418 419 145.4 0.1678 2.3647 0.1530
418 425 54.9 0.1615 2.6423 0.1530
419 420 70.3 0.1574 2.7906 0.1530
420 421 76.4 0.1345 0.7065 0.1230
420 422 85.8 0.2188 7.0590 0.1330
422 423 92.7 0.2852 6.8353 0.1000
422 424 88.5 0.5908 6.3748 0.1000
425 426 133.7 0.1231 0.9381 0.1230
425 427 97.3 0.1334 0.9812 0.1330
Constraint error in algorithm Lincs at step 531703
Step 531704, time 1063.41 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 7430.121582 (between atoms 399 and 400) rms 615.946228
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
291 292 49.8 0.1528 0.1751 0.1530
292 293 49.1 0.1248 0.1386 0.1250
292 294 89.7 0.1248 1.4936 0.1250
385 387 44.9 0.1468 0.2220 0.1470
387 388 43.4 0.1528 0.2223 0.1530
387 390 63.7 0.1529 5.2034 0.1530
390 391 57.4 0.1229 5.1592 0.1230
390 392 122.2 0.1333 5.5198 0.1330
392 393 67.7 0.1486 74.0389 0.1470
392 396 98.4 0.1472 4.4359 0.1470
393 394 75.9 0.1547 73.2845 0.1530
393 397 148.6 0.1580 71.4154 0.1530
394 395 101.8 0.1530 6.9962 0.1530
395 396 56.6 0.1529 2.1316 0.1530
397 398 68.8 0.1264 25.7745 0.1230
397 399 82.0 0.1473 745.0591 0.1330
399 400 85.0 0.1120 743.1122 0.1000
399 401 71.7 0.4113 756.2589 0.1470
401 402 63.6 0.4210 487.8731 0.1530
401 414 78.2 0.7868 851.3060 0.1530
402 403 86.8 0.1661 861.5334 0.1530
403 404 108.1 0.1543 75.6322 0.1530
404 405 77.1 0.1471 42.6452 0.1470
405 406 108.2 0.1000 2.0902 0.1000
405 407 122.6 0.1339 4.2094 0.1340
407 408 60.1 0.1339 2.8116 0.1340
407 411 58.5 0.1339 2.8097 0.1340
408 409 48.9 0.0999 0.1603 0.1000
408 410 49.1 0.0999 0.1606 0.1000
411 412 49.0 0.0999 0.1607 0.1000
411 413 49.7 0.0999 0.1627 0.1000
414 415 58.2 0.7741 124.7148 0.1230
414 416 114.9 2.1606 111.0335 0.1330
416 417 158.1 2.3135 40.3120 0.1000
416 418 162.7 3.0202 39.1527 0.1470
418 419 162.6 2.3618 23.2176 0.1530
418 425 146.8 2.6391 22.8310 0.1530
419 420 130.7 2.7872 11.2242 0.1530
420 421 119.4 0.7057 3.8447 0.1230
420 422 66.6 7.0503 5.1704 0.1330
422 423 89.0 6.8269 1.9886 0.1000
422 424 89.2 6.3670 2.8379 0.1000
425 426 151.7 0.9369 9.4031 0.1230
425 427 144.4 0.9800 9.8162 0.1330
427 428 138.6 0.1226 1.8137 0.1470
427 431 66.9 0.1116 1.6430 0.1470
428 432 45.0 0.1603 0.4833 0.1530
429 430 82.5 0.1534 0.0428 0.1530
430 431 109.2 0.1615 0.0695 0.1530
Constraint error in algorithm Lincs at step 531704
t = 1063.408 ps: Water molecule starting at atom 6070 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Step 531704 Warning: pressure scaling more than 1%, mu: 1.26865 1.26865 1.26865
There were 2 inconsistent shifts. Check your topology
Grid: 7 x 8 x 7 cells
Grid: -2147483648 x -2147483648 x -2147483648 cells
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
-------------- next part --------------
;
; User swetha
; FULL MOLECULAR DYNAMICS - Echi MUTANT D27W
;
title = Echi MUTANT D27W
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2000 ps.
nstcomm = 1
nstxout = 50
nstvout = 0
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 5
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = protein sol CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = protein sol CL-
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
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
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