hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is
------------------------------------------------------------------------------------------------------------------ step 4088520, will finish at Sat Sep 22 06:22:35 2007 Step 4088530, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 17.051964 (between atoms 615 and 616) rms 0.709711 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 613 614 35.7 0.1233 0.1232 0.1230 613 615 35.2 0.1332 0.1352 0.1330 615 616 90.0 0.0997 1.8052 0.1000 615 617 90.0 0.1322 1.3965 0.1000 step 4088530, will finish at Sat Sep 22 06:22:35 2007Warning: 1-4 interaction at distance larger than 1 These are ignored for the rest of the simulation turn on -debug for more information Step 4088531, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.625723 (between atoms 615 and 617) rms 0.062578 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 612 613 46.4 0.1548 0.1344 0.1530 613 614 37.2 0.1232 0.1816 0.1230 613 615 89.7 0.1352 0.2216 0.1330 615 616 76.3 1.8052 0.1476 0.1000 615 617 89.7 1.3965 0.2626 0.1000 Step 4088532, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 14.399930 (between atoms 615 and 616) rms 0.598937 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 611 612 44.2 0.1693 0.1761 0.1530 612 613 35.4 0.1344 0.1669 0.1530 613 614 95.7 0.1816 0.1308 0.1230 615 616 90.2 0.1476 1.5400 0.1000 615 617 90.5 0.2626 1.1927 0.1000 Step 4088533, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.051080 (between atoms 615 and 617) rms 0.046065 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 609 611 44.5 0.1529 0.1910 0.1470 611 612 39.9 0.1761 0.1800 0.1530 611 618 41.9 0.1579 0.1736 0.1530 612 613 105.9 0.1669 0.2124 0.1530 613 614 123.8 0.1308 0.1181 0.1230 613 615 34.6 0.1178 0.2224 0.1330 615 616 74.0 1.5400 0.1253 0.1000 615 617 80.3 1.1927 0.2051 0.1000 Step 4088534, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 45040.144531 (between atoms 613 and 614) rms 1994.670654 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 582 584 41.9 0.1470 0.2116 0.1470 584 585 41.3 0.1530 0.2102 0.1530 584 586 69.2 0.1530 8.3830 0.1530 586 587 59.2 0.1230 8.3382 0.1230 586 588 78.9 0.1331 28.5889 0.1330 588 589 75.7 0.1001 27.4635 0.1000 588 590 80.7 0.1471 156.4029 0.1470 590 591 82.5 0.1531 156.2125 0.1530 590 607 84.1 0.1537 272.5951 0.1530 591 592 78.3 0.1531 23.8232 0.1530 592 593 55.2 0.1330 6.7518 0.1330 592 595 55.7 0.1390 6.7401 0.1390 593 594 41.6 0.1090 0.1595 0.1090 593 596 45.1 0.1330 0.1971 0.1330 595 598 37.7 0.1390 0.1911 0.1390 595 599 34.4 0.1390 0.1923 0.1390 607 608 85.1 0.1235 322.3230 0.1230 607 609 90.8 0.1334 722.2238 0.1330 609 610 87.5 0.1001 730.5731 0.1000 609 611 91.7 0.1910 2220.5916 0.1470 611 612 113.1 0.1800 1928.0201 0.1530 611 618 61.9 0.1736 2612.3730 0.1530 612 613 152.6 0.2124 2170.9067 0.1530 613 614 95.0 0.1181 5540.0610 0.1230 613 615 100.8 0.2224 1264.8948 0.1330 615 616 88.0 0.1253 729.0342 0.1000 615 617 69.1 0.2051 610.1647 0.1000 618 619 96.0 0.1365 1772.1053 0.1230 618 620 101.8 0.1456 1954.0292 0.1330 620 621 97.1 0.1014 161.6277 0.1000 620 622 44.0 0.1484 387.2649 0.1470 622 623 119.2 0.1536 271.5126 0.1530 622 628 110.2 0.1536 303.3078 0.1530 623 624 65.6 0.1531 51.2406 0.1530 624 625 113.7 0.1530 26.6845 0.1530 625 626 32.7 0.1250 0.1557 0.1250 625 627 34.2 0.1250 0.1577 0.1250 628 629 78.5 0.1232 35.4732 0.1230 628 630 106.0 0.1331 32.5768 0.1330 630 631 111.3 0.1000 10.4951 0.1000 630 632 136.9 0.1471 10.4534 0.1470 632 633 34.5 0.1530 0.1991 0.1530 632 637 34.5 0.1530 0.2035 0.1530 Fatal error: Determinant = 25363147356027562275897344.000000 -------------------------------------------------------------------------------------------------- hear it is telling that bonds are rotating more than 30 degrees and showing LINCS error with respect to the relative constraint deviation and in some cases atom -1, atom-2 current value is much high compare to previous and determinent is also too high .is i need to keep any bond constriants? ,what is the reason for these error what changes should i do in my .mdp file so that i can over come these problems Hear my .mdp file ----------------------- ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES -DPOSRES_WATER integrator = md comm_mode = Angular dt = 0.002 ; ps ! nsteps = 5000000 ; total 10000 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 -------------------------- regards vijay kumar
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