Thanks Justin, now i have different problem when i run mdrun_d programme with the following command ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr -c 1HHO_md.gro -e md.edr -nt 1 i got error as follows Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.348354, max 2.293388 (between atoms 27 and 28) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 45 47 30.1 0.1250 0.0966 0.1250 45 46 89.4 0.1250 0.1611 0.1250 44 45 38.0 0.1530 0.1715 0.1530 36 37 89.8 0.1090 0.1977 0.1090 27 28 89.6 0.1090 0.3590 0.1090 18 19 89.1 0.1090 0.1375 0.1090 15 17 56.1 0.1250 0.1306 0.1250 6 7 89.2 0.1090 0.1781 0.1090 Wrote pdb files with previous and current coordinates
Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 6.925181, max 29.122365 (between atoms 9 and 10) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 45 47 95.4 0.0966 0.1734 0.1250 36 37 90.1 0.1977 1.6174 0.1090 27 28 90.1 0.3590 0.1991 0.1090 18 20 61.3 0.1422 0.0426 0.1400 18 19 91.3 0.1375 0.2554 0.1090 15 17 89.4 0.1306 0.1306 0.1250 11 18 86.8 0.1423 0.2272 0.1400 10 12 90.0 0.1542 4.1927 0.1530 10 11 89.4 0.1418 4.2147 0.1400 9 13 36.9 0.1545 0.2135 0.1530 9 10 89.3 0.1415 4.2171 0.1400 8 9 39.6 0.1422 0.1957 0.1400 6 7 89.3 0.1781 0.2107 0.1090 2 11 87.7 0.1404 0.2813 0.1380 Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 10 and 14 at distance 4.309 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 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1141861312104.288574, max 8387384410969.760742 (between atoms 36 and 37) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 114.2 0.2088 307491611.7030 0.2000 44 45 41.6 0.1457 0.1972 0.1530 43 44 129.5 0.1536 16995520.2978 0.1530 40 43 100.2 0.1544 526802811.8353 0.1530 40 41 115.4 0.1427 1126735523.3763 0.1400 39 42 110.6 0.1546 3296841333.8448 0.1530 39 40 95.3 0.1427 3867105914.6031 0.1400 38 39 103.0 0.1432 6773859895.7491 0.1400 36 38 97.4 0.1419 20921022161.9095 0.1400 36 37 89.9 1.6174 914224900795.8143 0.1090 34 35 105.4 0.1340 772011346.9170 0.1340 32 36 97.9 0.1434 21005542749.8526 0.1400 31 34 103.2 0.1533 4047716956.2246 0.1530 31 32 100.6 0.1407 6865225352.3692 0.1400 30 33 108.3 0.1530 640798229.9764 0.1530 30 31 99.0 0.1401 4174186935.5429 0.1400 29 30 120.6 0.1399 992312479.3422 0.1400 27 29 111.0 0.1429 1205532064.0067 0.1400 27 28 121.7 0.1991 412296837.5467 0.1090 25 26 78.4 0.1354 5.1420 0.1340 23 27 97.8 0.1457 412296831.0029 0.1400 22 25 106.1 0.1565 14.5779 0.1530 22 23 81.6 0.1448 15.7238 0.1400 21 24 98.1 0.1614 4.0101 0.1530 21 22 88.5 0.1472 15.3081 0.1400 20 21 95.2 0.1568 14.5247 0.1400 18 20 84.5 0.0426 15.1546 0.1400 18 19 90.3 0.2554 3.8535 0.1090 15 17 89.9 0.1306 4.2160 0.1250 15 16 90.0 0.1191 25.1978 0.1250 14 15 88.7 0.1553 3.4423 0.1530 13 14 97.9 0.1679 2.7244 0.1530 11 18 76.7 0.2272 23.5748 0.1400 10 12 170.5 4.1927 15.3594 0.1530 10 11 126.4 4.2147 26.6521 0.1400 9 13 51.9 0.2135 3.3106 0.1530 9 10 165.5 4.2171 16.1115 0.1400 8 9 76.6 0.1957 7.1674 0.1400 6 41 109.4 0.1477 1166436972.1222 0.1400 6 8 117.5 0.1602 406664611.1456 0.1400 6 7 135.7 0.2107 406664648.5804 0.1090 5 41 115.5 0.1408 3655729543.2299 0.1380 5 38 106.1 0.1421 6636732910.3252 0.1380 4 32 105.3 0.1409 6209428864.9749 0.1380 4 29 114.0 0.1420 4072911915.0192 0.1380 3 23 112.7 0.1483 125990964.2723 0.1380 3 20 130.8 0.1584 125990986.2569 0.1380 2 11 45.9 0.2813 96334844.6580 0.1380 2 8 153.6 0.1399 96334840.9361 0.1380 1 5 101.1 0.1999 3861844055.9208 0.2000 1 4 99.4 0.2050 4350154899.2293 0.2000 1 3 120.9 0.2049 276545143.5239 0.2000 Wrote pdb files with previous and current coordinates Segmentation fault i am using the following .mdp files title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = no ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 3 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = HEM AL OXY ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310 ; Pressure coupling is on ;Pcoupl = Parrinello-Rahman ;pcoupltype = isotropic ;tau_p = 1.0 ;compressibility = 4.5e-5 ;ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance pull_dim = N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Fe pull_group1 = O1 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 I am expecting your reply thanks in advance
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