[gmx-users] Molecular dynamcis simualtion regarding
rekkha nivethitha
rnnive at gmail.com
Wed Aug 18 11:05:59 CEST 2010
Hi frnds,
On running, Molecular dynamics simulation of protein-protein complex, While
running md run, i got this error,
*
"Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5#
Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5#
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.011042, max 4.472447 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15#
- Show quoted text -
Wrote pdb files with previous and current coordinates
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.068209, max 23.054199 (between atoms 10 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
37 39 51.4 0.0589 0.1043 0.1360
37 38 46.0 0.0457 0.0811 0.1230
34 36 67.7 0.0255 0.1339 0.1530
34 35 69.4 0.0269 0.1376 0.1530
33 37 77.9 0.4780 0.1629 0.1530
33 34 97.4 0.4847 0.1141 0.1530
31 33 103.3 0.2087 0.4628 0.1470
31 32 63.0 0.1981 0.0359 0.1000
29 31 70.6 0.4388 0.2060 0.1330
29 30 54.5 0.2491 0.1016 0.1230
25 28 167.9 0.1444 0.0334 0.1530
25 26 140.5 0.1344 0.0404 0.1430
24 29 101.6 0.3497 0.2598 0.1530
24 25 42.7 0.2115 0.2662 0.1530
22 24 60.8 0.3511 0.2556 0.1470
22 23 91.3 0.1603 0.1401 0.1000
20 22 86.3 0.1443 1.1227 0.1330
20 21 134.2 0.1908 0.8440 0.1230
17 19 173.1 0.4358 1.5698 0.1530
17 18 173.5 0.4358 1.5704 0.1530
16 20 174.6 0.6605 2.0535 0.1530
16 17 177.4 0.3602 2.8668 0.1530
14 16 168.8 0.2643 2.9856 0.1470
14 15 166.1 0.3248 1.9914 0.1000
12 14 176.2 0.7278 3.1437 0.1330
12 13 177.0 0.3443 2.5072 0.1230
10 12 174.8 0.3544 3.6803 0.1530
10 11 169.2 0.4052 1.7864 0.1530
8 10 173.1 0.5139 1.8491 0.1470
8 9 151.4 0.0964 0.7325 0.1000
6 8 115.1 0.0879 0.8155 0.1330
6 7 53.8 0.1958 0.0677 0.1230
4 5 56.9 0.1444 0.0413 0.1530
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.16#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.16#
Wrote pdb files with previous and current coordinates
starting mdrun 'Protein'
10000 steps, 20.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.511037, max 177.073975 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
39 40 104.8 0.1585 0.1484 0.1000
37 39 147.0 0.0589 0.6971 0.1360
37 38 177.1 0.0457 0.6713 0.1230
34 36 158.3 0.0255 0.7496 0.1530
34 35 159.0 0.0269 0.7308 0.1530
33 37 162.2 0.4780 0.9895 0.1530
33 34 173.7 0.4847 0.9904 0.1530
31 33 115.7 0.2087 0.9548 0.1470
31 32 177.0 0.1981 0.3387 0.1000
29 31 128.4 0.4388 0.2813 0.1330
29 30 159.0 0.2491 0.2681 0.1230
24 29 105.7 0.3497 0.6145 0.1530
24 25 105.5 0.2115 0.3658 0.1530
22 24 90.5 0.3511 0.3786 0.1470
22 23 75.8 0.1603 0.1584 0.1000
20 22 85.7 0.1443 4.4331 0.1330
20 21 146.2 0.1908 4.6893 0.1230
17 19 172.3 0.4358 11.1229 0.1530
17 18 172.6 0.4358 11.1267 0.1530
16 20 172.6 0.6605 15.2461 0.1530
16 17 178.1 0.3602 20.4103 0.1530
14 16 173.5 0.2643 20.5192 0.1470
14 15 170.9 0.3248 14.1432 0.1000
12 14 174.8 0.7278 23.6838 0.1330
12 13 177.4 0.3443 18.2694 0.1230
10 12 175.8 0.3544 26.0403 0.1530
10 11 168.9 0.4052 13.2549 0.1530
8 10 174.1 0.5139 13.7575 0.1470
8 9 163.8 0.0964 4.7575 0.1000
6 8 125.8 0.0879 4.2261 0.1330
6 7 148.2 0.1958 0.9645 0.1230
4 6 149.4 0.2692 0.7665 0.1530
129611 129612 90.0 0.1360 0.2674 0.1360
129612 129613 90.0 0.1000 0.1416 0.1000
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.17#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.17#
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 1 and 8 at distance 3.642 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 217610 and 217611)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
39 40 122.2 0.1484 5268.9219 0.1000
37 39 172.1 0.6971 24781.9824 0.1360
37 38 177.4 0.6713 25114.8770 0.1230
34 36 176.9 0.7496 24894.9922 0.1530
34 35 176.8 0.7308 24889.9258 0.1530
33 37 174.8 0.9895 71015.7422 0.1530
33 34 176.6 0.9904 71153.2344 0.1530
31 33 148.3 0.9548 107354.2266 0.1470
31 32 162.9 0.3387 229725.0156 0.1000
29 31 121.9 0.2813 1073675.7500 0.1330
29 30 148.5 0.2681 789798.5000 0.1230
26 27 50.0 0.0775 9266.4717 0.1000
25 28 100.1 0.2466 738411.5000 0.1530
25 26 98.7 0.2343 746187.6875 0.1430
3026 3028 91.9 0.1250 0.4201 0.1250
3026 3027 90.1 0.1250 6.0161 0.1250
3025 3026 92.0 0.1530 0.3814 0.1530
3024 3025 93.8 0.1530 0.0507 0.1530
121875 121876 46.4 0.1000 0.0998 0.1000
129545 129546 90.0 0.1360 105344.8516 0.1360
129546 129547 90.0 0.1000 31176.9414 0.1000
129611 129612 90.0 0.2674 0.1382 0.1360
129612 129613 90.0 0.1416 0.3485 0.1000
129806 129807 90.0 0.1361 0.1366 0.1360
129807 129808 90.0 0.0997 0.1412 0.1000
209585 209586 90.0 0.1360 382829.5000 0.1360
209586 209587 90.0 0.1000 3123167.5000 0.1000
209624 209625 90.0 0.1360 4163099951104.0000 0.1360
209625 209626 90.0 0.1000 160979585335296.0000 0.1000
209747 209748 90.0 0.1360 12586.1602 0.1360
209748 209749 90.0 0.1000 7844.0381 0.1000
209774 209775 90.0 0.1360 3.7737 0.1360
209775 209776 90.0 0.1000 47.2691 0.1000
209789 209790 90.0 0.1360 14.4135 0.1360
209790 209791 90.0 0.1000 104.0994 0.1000
209879 209880 51.9 0.1360 0.1343 0.1360
209880 209881 41.7 0.1000 0.0874 0.1000
209897 209898 90.0 0.1360 120248.1172 0.1360
209898 209899 90.0 0.1000 138503.4844 0.1000
209930 209931 90.0 0.1360 63489.3242 0.1360
209931 209932 90.0 0.1000 47976.7461 0.1000
210014 210015 90.0 0.1360 137179.0312 0.1360
210015 210016 90.0 0.1000 71803.4219 0.1000
210050 210051 90.0 0.1360 213452947456.0000 0.1360
210051 210052 90.0 0.1000 72714027008.0000 0.1000
210056 210057 90.0 0.1360 199.7133 0.1360
210057 210058 90.0 0.1000 105.5468 0.1000
210098 210099 90.0 0.1360 73437.0312 0.1360
210099 210100 90.0 0.1000 268403.0625 0.1000
210164 210165 90.0 0.1360 46437.6328 0.1360
210165 210166 90.0 0.1000 51395.5938 0.1000
210179 210180 90.0 0.1360 4295428199677952.0000 0.1360
210180 210181 90.0 0.1000 486194794201088.0000 0.1000
210182 210183 90.0 0.1360 56.3336 0.1360
210183 210184 90.0 0.1000 44.0229 0.1000
210257 210258 90.0 0.1360 0.6066 0.1360
210258 210259 90.0 0.1000 0.3301 0.1000
210266 210267 90.0 0.1360 203980400752590848.0000 0.1360
210267 210268 90.0 0.1000 13299902656299401216.0000 0.1000
210278 210279 90.0 0.1360 12786.2998 0.1360
210279 210280 90.0 0.1000 3739.4780 0.1000
210281 210282 90.0 0.1360 1347.9357 0.1360
210282 210283 90.0 0.1000 288.4388 0.1000
210335 210336 90.0 0.1360 0.8601 0.1360
210336 210337 90.0 0.1000 24.9081 0.1000
210344 210345 90.0 0.1360 9.9901 0.1360
210345 210346 90.0 0.1000 1.1741 0.1000
210401 210402 90.0 0.1360 27811495937048576.0000 0.1360
210402 210403 90.0 0.1000 840865673553903616.0000 0.1000
210405 210406 90.0 0.1000 0.2518 0.1000
210420 210421 90.0 0.1000 0.8193 0.1000
210455 210456 90.0 0.1360 13482.6270 0.1360
210456 210457 90.0 0.1000 792207.0625 0.1000
210464 210465 56.8 0.1360 0.1316 0.1360
210465 210466 90.0 0.1000 6.4574 0.1000
217001 217002 90.0 0.1360 13.7040 0.1360
217002 217003 90.0 0.1000 39.0037 0.1000
217100 217101 90.0 0.1360 47.7831 0.1360
217101 217102 90.0 0.1000 28.3606 0.1000
217184 217185 90.0 0.1360 3.4058 0.1360
217185 217186 90.0 0.1000 0.9996 0.1000
217199 217200 90.0 0.1360 3054621.5000 0.1360
217200 217201 90.0 0.1000 3108384.5000 0.1000
217296 217297 61.5 0.1000 0.0997 0.1000
217334 217335 90.0 0.1360 0.9596 0.1360
217335 217336 90.0 0.1000 1.0436 0.1000
217340 217341 90.0 0.1360 3087.8428 0.1360
217341 217342 90.0 0.1000 170736.0938 0.1000
217364 217365 90.0 0.1360 0.1587 0.1360
217365 217366 90.0 0.1000 0.1284 0.1000
217370 217371 90.0 0.1360 13.5364 0.1360
217371 217372 90.0 0.1000 43.8809 0.1000
217418 217419 90.0 0.1360 18.2625 0.1360
217419 217420 90.0 0.1000 78.1691 0.1000
217421 217422 90.0 0.1360 7457577.0000 0.1360
217422 217423 90.0 0.1000 201796896.0000 0.1000
217451 217452 90.0 0.1360 326.0662 0.1360
217452 217453 90.0 0.1000 727.6672 0.1000
217484 217485 90.0 0.1360 4946.5952 0.1360
217485 217486 90.0 0.1000 3379.7615 0.1000
217523 217524 90.0 0.1360 151100137144320.0000 0.1360
217524 217525 90.0 0.1000 132571228798976.0000 0.1000
217529 217530 90.0 0.1360 39939540.0000 0.1360
217530 217531 90.0 0.1000 34472400.0000 0.1000
217553 217554 90.0 0.1360 1316.5348 0.1360
217554 217555 90.0 0.1000 25330.9297 0.1000
217565 217566 90.0 0.1360 5555419611136.0000 0.1360
217566 217567 90.0 0.1000 4930378661888.0000 0.1000
217571 217572 90.0 0.1360 0.1916 0.1360
217572 217573 90.0 0.1000 0.1029 0.1000
217589 217590 90.0 0.1360 2813.3743 0.1360
217590 217591 90.0 0.1000 29037.5332 0.1000
217607 217608 90.0 0.1360 327.0599 0.1360
217608 217609 90.0 0.1000 14864.0811 0.1000
217610 217611 90.0 0.1360 923021436809913529434302840832
.0000 0.1360
217611 217612 90.0 0.1000 32989325964921177052496789504.
0000
0.1000
217646 217647 90.0 0.1360 6619.4277 0.1360
217647 217648 90.0 0.1000 692045.7500 0.1000
217649 217650 90.0 0.1360 0.4602 0.1360
217650 217651 90.0 0.1000 0.8503 0.1000
217656 217657 46.3 0.1000 0.1009 0.1000
217694 217695 90.0 0.1360 20395.2773 0.1360
217695 217696 90.0 0.1000 3979995.7500 0.1000
217700 217701 90.0 0.1360 39071502175305728.0000 0.1360
217701 217702 90.0 0.1000 6424830840668160.0000 0.1000
217706 217707 90.0 0.1360 2210.6899 0.1360
217707 217708 90.0 0.1000 16389.5410 0.1000
217760 217761 90.0 0.1360 857911.1250 0.1360
217761 217762 90.0 0.1000 802024.6250 0.1000
217763 217764 90.0 0.1360 7892.6123 0.1360
217764 217765 90.0 0.1000 20200.1191 0.1000
217766 217767 90.0 0.1360 0.1947 0.1360
217767 217768 90.0 0.1000 11.7431 0.1000
217848 217849 90.0 0.1000 0.4890 0.1000
217860 217861 90.0 0.1000 4.7575 0.1000
217892 217893 90.0 0.1360 0.1850 0.1360
217893 217894 33.6 0.1000 0.1197 0.1000
217919 217920 90.0 0.1360 4411960316436235384801722368.0000
0.1360
217920 217921 90.0 0.1000 1212861174208338075609726976.0000
0.1000
217923 217924 90.0 0.1000 0.2532 0.1000
217937 217938 90.0 0.1360 1890087.1250 0.1360
217938 217939 90.0 0.1000 2544109.2500 0.1000
217940 217941 90.0 0.1360 3761396.7500 0.1360
217941 217942 90.0 0.1000 233782.6875 0.1000
Back Off! I just backed up step1b.pdb to ./#step1b.pdb.5#
Back Off! I just backed up step1c.pdb to ./#step1c.pdb.5#
Wrote pdb files with previous and current coordinates
Segmentation fault"
*What is the problem behind this error.
Why its coming..
I used this parameter file:*
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.135
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
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
Can u help me in, how to rectify this problem and find a suitable solution
to the problem.
Thank u in advance.
--
S.T.B. Rekkha Nivethitha
MPhil, Department of Bioinformatics,
Structural Biology Lab,
Bharathiar University,
Coimbatore - 46.
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