Hi, all
when I use:
grompp -f em_constrain.mdp -c provin_solv_ion.pdb -p provin_1dxo.top -o
bovin_em.tpr
mdrun -v -s bovin_em.tpr -nt 2 -deffnm em_constrain
get the result:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 2000
Step= 0, Dmax= 1.0e-02 nm, Epot= -3.50527e+05 Fmax= 1.98713e+04, atom=
21002
Step= 1, Dmax= 1.0e-02 nm, Epot= -3.68529e+05 Fmax= 9.78841e+03, atom=
3050
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.87513e+05 Fmax= 5.86618e+03, atom=
1142
Step= 3, Dmax= 1.4e-02 nm, Epot= -4.04229e+05 Fmax= 3.50892e+03, atom=
1142
Step= 4, Dmax= 1.7e-02 nm, Epot= -4.20673e+05 Fmax= 1.79695e+03, atom=
29070
Step= 5, Dmax= 2.1e-02 nm, Epot= -4.39433e+05 Fmax= 1.41541e+03, atom=
29070
Step= 6, Dmax= 2.5e-02 nm, Epot= -4.54148e+05 Fmax= 3.62694e+03, atom=
919
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.58532e+05 Fmax= 4.18232e+03, atom=
919
Step 8, time 0.016 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002283, max 0.104367 (between atoms 919 and 920)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
917 919 32.2 0.1385 0.1443 0.1340
919 923 32.9 0.1382 0.1442 0.1340
919 920 39.7 0.1385 0.1480 0.1340
920 921 33.9 0.1014 0.1067 0.1000
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.60091e+05 Fmax= 6.02658e+03, atom= 31
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004622, max 0.121975 (between atoms 371 and 375)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005013, max 0.133287 (between atoms 34 and 38)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
425 429 30.4 0.1400 0.1479 0.1390
429 431 30.3 0.1399 0.1481 0.1390
422 425 30.6 0.1400 0.1477 0.1390
422 423 30.7 0.1400 0.1478 0.1390
34 38 40.6 0.1428 0.1575 0.1390
427 431 30.9 0.1399 0.1482 0.1390
38 40 39.9 0.1425 0.1563 0.1390
31 34 39.9 0.1430 0.1566 0.1390
31 32 38.9 0.1430 0.1552 0.1390
32 36 38.7 0.1426 0.1556 0.1390
36 40 39.0 0.1422 0.1557 0.1390
259 261 35.0 0.1403 0.1518 0.1390
252 255 35.6 0.1406 0.1516 0.1390
423 427 30.9 0.1400 0.1482 0.1390
252 253 35.4 0.1406 0.1516 0.1390
253 257 34.7 0.1405 0.1517 0.1390
255 259 35.3 0.1405 0.1520 0.1390
257 261 34.6 0.1404 0.1516 0.1390
1102 1106 36.1 0.1407 0.1530 0.1390
1106 1108 35.8 0.1407 0.1526 0.1390
1099 1102 36.0 0.1408 0.1523 0.1390
1099 1100 35.4 0.1408 0.1518 0.1390
1100 1104 36.0 0.1407 0.1528 0.1390
1104 1108 36.3 0.1406 0.1529 0.1390
366 369 38.0 0.1461 0.1540 0.1390
366 367 38.2 0.1462 0.1546 0.1390
367 371 39.9 0.1456 0.1558 0.1390
369 373 39.1 0.1455 0.1548 0.1390
371 375 41.1 0.1442 0.1560 0.1390
373 375 40.5 0.1440 0.1555 0.1390
917 919 30.6 0.1443 0.1434 0.1340
919 923 30.4 0.1442 0.1438 0.1340
919 920 40.5 0.1480 0.1482 0.1340
920 922 35.4 0.1064 0.1071 0.1000
920 921 35.8 0.1067 0.1073 0.1000
Step= 10, Dmax= 2.1e-02 nm, Epot= -4.64146e+05 Fmax= 3.09226e+03, atom=
1016
Step= 11, Dmax= 2.6e-02 nm, Epot= -4.64176e+05 Fmax= 6.03740e+03, atom=
252
Step= 12, Dmax= 3.1e-02 nm, Epot= -4.66478e+05 Fmax= 5.71954e+03, atom=
582
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004522, max 0.099878 (between atoms 273 and 277)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005964, max 0.095520 (between atoms 582 and 585)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
425 429 33.0 0.1457 0.1506 0.1390
429 431 33.0 0.1459 0.1503 0.1390
422 425 32.8 0.1456 0.1504 0.1390
422 423 33.2 0.1458 0.1508 0.1390
259 261 33.4 0.1463 0.1507 0.1390
252 255 34.5 0.1465 0.1518 0.1390
252 253 34.3 0.1465 0.1517 0.1390
253 257 33.8 0.1464 0.1515 0.1390
255 259 33.8 0.1466 0.1515 0.1390
257 261 33.6 0.1462 0.1508 0.1390
34 38 32.7 0.1427 0.1501 0.1390
427 431 33.0 0.1461 0.1505 0.1390
38 40 31.8 0.1426 0.1493 0.1390
31 34 33.2 0.1425 0.1501 0.1390
31 32 33.0 0.1421 0.1501 0.1390
32 36 32.8 0.1423 0.1498 0.1390
36 40 32.1 0.1424 0.1488 0.1390
423 427 33.5 0.1461 0.1511 0.1390
440 443 34.6 0.1434 0.1513 0.1390
440 441 34.6 0.1434 0.1513 0.1390
441 445 34.0 0.1432 0.1515 0.1390
445 449 34.3 0.1432 0.1509 0.1390
582 585 35.3 0.1436 0.1523 0.1390
582 583 35.9 0.1436 0.1521 0.1390
443 447 33.6 0.1433 0.1513 0.1390
583 587 35.0 0.1433 0.1520 0.1390
585 589 34.0 0.1434 0.1515 0.1390
587 591 33.7 0.1432 0.1513 0.1390
160 164 34.1 0.1427 0.1518 0.1390
162 166 33.1 0.1427 0.1512 0.1390
589 591 33.2 0.1433 0.1507 0.1390
164 168 34.2 0.1428 0.1509 0.1390
1017 1021 34.3 0.1466 0.1516 0.1390
166 168 34.0 0.1427 0.1507 0.1390
447 449 33.8 0.1433 0.1506 0.1390
270 273 35.4 0.1448 0.1520 0.1390
270 271 35.1 0.1443 0.1526 0.1390
271 275 35.0 0.1443 0.1524 0.1390
1016 1019 34.9 0.1467 0.1520 0.1390
273 277 35.3 0.1448 0.1529 0.1390
1016 1017 35.8 0.1470 0.1520 0.1390
275 279 34.5 0.1447 0.1508 0.1390
1019 1023 33.4 0.1463 0.1511 0.1390
277 279 34.5 0.1447 0.1519 0.1390
1021 1025 33.2 0.1461 0.1511 0.1390
1023 1025 33.2 0.1462 0.1507 0.1390
159 162 34.9 0.1429 0.1518 0.1390
159 160 35.8 0.1429 0.1523 0.1390
1102 1106 34.1 0.1463 0.1516 0.1390
1106 1108 34.0 0.1462 0.1515 0.1390
1099 1102 34.6 0.1461 0.1516 0.1390
1099 1100 34.5 0.1460 0.1519 0.1390
1100 1104 34.0 0.1463 0.1515 0.1390
1104 1108 34.1 0.1464 0.1512 0.1390
Step= 14, Dmax= 1.9e-02 nm, Epot= -4.69749e+05 Fmax= 4.07991e+03, atom=
252
Step= 15, Dmax= 2.2e-02 nm, Epot= -4.69925e+05 Fmax= 5.60899e+03, atom=
261
Step= 16, Dmax= 2.7e-02 nm, Epot= -4.70705e+05 Fmax= 5.45189e+03, atom=
252
Step= 18, Dmax= 1.6e-02 nm, Epot= -4.73964e+05 Fmax= 2.48190e+03, atom=
261
Step= 20, Dmax= 9.6e-03 nm, Epot= -4.74966e+05 Fmax= 2.70939e+03, atom=
252
Step= 21, Dmax= 1.2e-02 nm, Epot= -4.75907e+05 Fmax= 2.89559e+03, atom=
261
Step= 22, Dmax= 1.4e-02 nm, Epot= -4.76591e+05 Fmax= 3.99485e+03, atom=
252
Step= 23, Dmax= 1.7e-02 nm, Epot= -4.77447e+05 Fmax= 4.04995e+03, atom=
159
Step= 24, Dmax= 2.0e-02 nm, Epot= -4.77488e+05 Fmax= 5.14109e+03, atom=
159
Step= 25, Dmax= 2.4e-02 nm, Epot= -4.77732e+05 Fmax= 5.38157e+03, atom=
159
Step= 27, Dmax= 1.4e-02 nm, Epot= -4.80794e+05 Fmax= 1.66386e+03, atom=
159
Step= 29, Dmax= 8.6e-03 nm, Epot= -4.81524e+05 Fmax= 2.89830e+03, atom=
159
Step= 30, Dmax= 1.0e-02 nm, Epot= -4.82318e+05 Fmax= 2.35166e+03, atom=
159
Step= 31, Dmax= 1.2e-02 nm, Epot= -4.82749e+05 Fmax= 3.86449e+03, atom=
159
Step= 32, Dmax= 1.5e-02 nm, Epot= -4.83525e+05 Fmax= 3.49726e+03, atom=
159
Step= 34, Dmax= 8.9e-03 nm, Epot= -4.84525e+05 Fmax= 1.11416e+03, atom=
159
Step= 35, Dmax= 1.1e-02 nm, Epot= -4.85311e+05 Fmax= 3.96327e+03, atom=
159
Step= 36, Dmax= 1.3e-02 nm, Epot= -4.86295e+05 Fmax= 2.41624e+03, atom=
159
Step= 38, Dmax= 7.7e-03 nm, Epot= -4.86920e+05 Fmax= 1.60263e+03, atom=
159
Step= 39, Dmax= 9.3e-03 nm, Epot= -4.87412e+05 Fmax= 3.14316e+03, atom=
159
Step= 40, Dmax= 1.1e-02 nm, Epot= -4.88053e+05 Fmax= 2.47491e+03, atom=
159
Step= 41, Dmax= 1.3e-02 nm, Epot= -4.88222e+05 Fmax= 4.11196e+03, atom=
159
Step= 42, Dmax= 1.6e-02 nm, Epot= -4.88825e+05 Fmax= 3.73410e+03, atom=
159
Step= 44, Dmax= 9.6e-03 nm, Epot= -4.89765e+05 Fmax= 1.20178e+03, atom=
159
Step= 45, Dmax= 1.2e-02 nm, Epot= -4.90094e+05 Fmax= 4.22621e+03, atom=
159
Step= 46, Dmax= 1.4e-02 nm, Epot= -4.91028e+05 Fmax= 2.55233e+03, atom=
159
Step= 48, Dmax= 8.3e-03 nm, Epot= -4.91564e+05 Fmax= 1.78402e+03, atom=
159
Step= 49, Dmax= 1.0e-02 nm, Epot= -4.91831e+05 Fmax= 3.28629e+03, atom=
159
Step= 50, Dmax= 1.2e-02 nm, Epot= -4.92363e+05 Fmax= 2.73460e+03, atom=
159
Step= 52, Dmax= 7.2e-03 nm, Epot= -4.92922e+05 Fmax= 9.94135e+02, atom=
159
writing lowest energy coordinates.
Back Off! I just backed up em_constrain.gro to ./#em_constrain.gro.1#
Steepest Descents converged to Fmax < 1000 in 53 steps
Potential Energy = -4.9292250e+05
Maximum force = 9.9413483e+02 on atom 159
Norm of force = 6.9268021e+01
There are 4 LINCS WARNING at :
1.Gly273-Ser277
2.Gln582-Gln585
3.Gly34-Gly38
4.Asn919-Asn920
They are all bonds that rotated more than 30 degrees
my .mdp :
title = bovin
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
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
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep =0.01
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = No
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; Pressure coupling
Pcoupl = No
Pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 293
gen-seed = 173529
I known something wrong in my system, but I don't known where it is ?
Could you help me to find it out? Thank you very much!
maggin
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