[gmx-users] "MD simulation of protein-protein complex"
XAvier Periole
x.periole at rug.nl
Tue Aug 17 13:36:59 CEST 2010
That means that in your starting conformation you have strong forces
probably coming from back contacts.
minimization/equilibration should help removing them.
On Aug 17, 2010, at 12:29 PM, rekkha nivethitha wrote:
> 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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