[gmx-users] Re: MD Simulation regarding
XAvier Periole
x.periole at rug.nl
Wed Aug 18 08:58:40 CEST 2010
Hi Rekkha,
you better off sending your post on the list to get comments from
more people.
If your are new in MD simulations and gromacs. The best for you is
to go through a couple of tutorials of protein simulations. I do not
know a links by heart but I am sure by searching the archive of
gromacs user-list or using google you'll find what you need.
Good luck,
XAvier.
On Aug 18, 2010, at 8:50 AM, rekkha nivethitha wrote:
>
> Dear Sir,
>
> Yesterday , i posted one query in gmx-users list: Such as,
>
> "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."
>
> For this query, u replied as:
>
>
> "That means that in your starting conformation you have strong forces
> probably coming from back contacts.
>
> minimization/equilibration should help removing them."
>
>
> But, Sorry Sir,
>
> I couldn get, what u r suggesting.. Am not clear in this..
>
> Can u explain in brief...
>
> How to do minimization or equilibration..
> U mean that, have to proceed the previous step again?
>
> Am new to MD simulation..
> Pls help me...
>
> I posted this as reply message, but the message is not posted, so
> only i send mail to ur ID.
> Pls, help me in solving the problem.. very urgent .....
>
> Thank u..
>
>
> --
> S.T.B. Rekkha Nivethitha
> MPhil, Department of Bioinformatics,
> Structural Biology Lab,
> Bharathiar University,
> Coimbatore - 46.
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