Dear Gromacs user, After I give the command for nvt, I get the following error: starting mdrun 'Protein in water' 150000 steps, 300.0 ps.
Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.410417, max 7.601056 (between atoms 188 and 192) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 177 179 40.7 0.1342 0.2195 0.1330 179 181 69.6 0.1484 0.2977 0.1470 179 180 51.1 0.1005 0.1744 0.1000 181 195 75.8 0.1543 0.2575 0.1530 181 182 77.0 0.1549 0.6596 0.1530 182 183 47.8 0.1549 0.3570 0.1530 183 186 76.8 0.1407 1.1049 0.1390 183 184 76.1 0.1406 0.9974 0.1390 186 187 69.8 0.1097 0.3696 0.1090 188 192 79.1 0.1403 1.1955 0.1390 188 189 72.0 0.1099 0.3759 0.1090 190 192 77.9 0.1404 1.1212 0.1390 190 191 71.5 0.1099 0.3818 0.1090 195 197 34.8 0.1345 0.1997 0.1330 195 196 39.9 0.1237 0.1807 0.1230 4571 4569 40.0 0.1404 0.0953 0.1400 4570 4569 91.2 0.1245 0.1846 0.1230 4572 4571 31.3 0.1005 0.1253 0.1000 184 188 41.1 0.1397 0.2396 0.1390 184 185 72.1 0.1097 0.4012 0.1090 193 194 82.9 0.1015 0.6012 0.1000 Wrote pdb files with previous and current coordinates step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2524.656192, max 85802.020979 (between atoms 170 and 177) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 170 177 81.9 0.1793 13127.8622 0.1530 177 179 94.9 0.2195 12873.2695 0.1330 179 181 88.6 0.2977 4411.0838 0.1470 181 195 96.6 0.2575 963.1998 0.1530 195 197 87.4 0.1997 250.2422 0.1330 195 196 80.6 0.1807 246.3256 0.1230 181 182 83.5 0.6596 33817.6412 0.1530 182 183 90.9 0.3570 1629245.5886 0.1530 179 180 150.7 0.1744 806.4780 0.1000 177 178 86.5 0.1487 13025.8466 0.1230 170 171 123.7 0.1636 1099.0521 0.1530 172 174 112.9 0.1334 124.2084 0.1330 172 173 119.8 0.1234 122.9154 0.1230 174 176 41.3 0.1000 19.2568 0.1000 141 149 30.5 0.1530 0.1924 0.1530 149 151 125.2 0.1330 18.9674 0.1330 149 150 34.1 0.1230 0.1614 0.1230 151 153 35.8 0.1471 28.7745 0.1470 151 152 83.3 0.1000 18.9746 0.1000 166 167 115.5 0.1238 341.2685 0.1230 153 166 117.8 0.1538 365.5008 0.1530 153 154 37.0 0.1531 14.8979 0.1530 154 155 90.8 0.1530 15.6791 0.1530 155 158 33.4 0.1390 0.1782 0.1390 155 156 32.8 0.1390 0.1771 0.1390 168 170 141.4 0.1596 1274.6369 0.1470 168 169 93.7 0.1015 232.5375 0.1000 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12958124.333813, max 292691795.227618 (between atoms 184 and 188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 203 204 32.1 0.1470 0.1744 0.1470 201 202 74.0 0.1532 1.1957 0.1530 202 203 117.7 0.1530 0.3991 0.1530 208 210 59.2 0.1359 3.5580 0.1330 208 209 73.2 0.1256 1.9933 0.1230 210 212 74.8 0.1480 1.9178 0.1470 210 211 93.8 0.1007 1.5815 0.1000 177 179 94.9 0.2195 12873.2691 0.1330 177 178 86.5 0.1487 13025.8467 0.1230 170 177 81.9 0.1793 13127.8623 0.1530 170 171 123.7 0.1636 1099.0521 0.1530 172 174 112.9 0.1334 124.2084 0.1330 174 176 41.3 0.1000 19.2568 0.1000 172 173 119.8 0.1234 122.9154 0.1230 168 170 141.4 0.1596 1274.6369 0.1470 168 169 93.7 0.1015 232.5375 0.1000 166 167 115.5 0.1238 341.2681 0.1230 153 166 117.8 0.1538 365.5039 0.1530 153 154 37.0 0.1531 14.8978 0.1530 151 153 35.8 0.1471 28.7776 0.1470 179 181 88.6 0.2977 4411.0814 0.1470 179 180 150.7 0.1744 806.4798 0.1000 212 217 118.1 0.1531 1.2961 0.1530 212 213 109.4 0.1531 1.3254 0.1530 213 214 39.0 0.1530 0.2085 0.1530 155 156 32.8 0.1390 0.1771 0.1390 155 158 33.4 0.1390 0.1782 0.1390 154 155 90.8 0.1530 15.6794 0.1530 151 152 83.3 0.1000 18.9666 0.1000 149 151 125.2 0.1330 18.9811 0.1330 4555 4554 30.1 0.1054 0.0939 0.1000 4569 4556 74.8 0.0906 0.1937 0.1390 181 195 96.6 0.2575 963.1279 0.1530 181 182 83.5 0.6596 33817.6442 0.1530 182 183 90.9 0.3570 1629245.5155 0.1530 183 186 90.6 1.1049 1615814.4351 0.1390 183 184 90.0 0.9974 40335415.9560 0.1390 186 190 96.9 0.1988 560191.7122 0.1390 186 187 88.8 0.3696 201776.9576 0.1090 188 192 67.5 1.1955 1821775.8654 0.1390 188 189 101.2 0.3759 1696383.9645 0.1090 190 192 81.7 1.1212 1424433.0456 0.1390 190 191 87.4 0.3818 426096.7655 0.1090 195 197 87.4 0.1997 250.1707 0.1330 195 196 80.6 0.1807 246.3559 0.1230 197 199 115.6 0.1672 46.7731 0.1470 197 198 93.5 0.1195 71.3260 0.1000 199 208 110.1 0.1646 12.2018 0.1530 199 200 126.5 0.1592 13.4121 0.1530 4571 4569 57.6 0.0953 0.1778 0.1400 4570 4569 96.5 0.1846 0.0942 0.1230 4573 4571 129.0 0.1855 14090.0537 0.1480 4572 4571 57.4 0.1253 0.1613 0.1000 184 188 89.7 0.2396 40684159.6756 0.1390 184 185 90.6 0.4012 30909138.0053 0.1090 4581 4573 111.6 0.1449 80915.8503 0.1390 4574 4573 76.0 0.1584 14090.0686 0.1530 4575 4574 42.1 0.1584 0.2180 0.1530 4583 4581 115.9 0.1482 189006.2806 0.1400 4582 4581 101.5 0.1307 86465.6939 0.1230 4585 4583 96.2 0.1493 1521854.0321 0.1480 4584 4583 100.1 0.1012 212428.0383 0.1000 217 219 33.2 0.1331 0.1875 0.1330 217 218 39.2 0.1230 0.1766 0.1230 432 433 90.0 0.1090 4.9068 0.1090 4693 4691 33.2 0.1400 0.1794 0.1400 4695 4693 113.6 0.1390 48586.2542 0.1390 4694 4693 32.2 0.1230 0.1573 0.1230 4704 4702 109.2 0.1400 941999.6432 0.1400 4703 4702 107.8 0.1000 247420.2683 0.1000 4706 4704 97.5 0.1390 3171125.9217 0.1390 4705 4704 107.2 0.1230 927537.6196 0.1230 4707 4706 95.6 0.1480 2865230.8599 0.1480 4709 4707 106.5 0.1400 1358764.5608 0.1400 4708 4707 100.7 0.1000 1219377.5021 0.1000 4702 4695 101.5 0.1480 271922.1291 0.1480 4696 4695 99.4 0.1530 48586.2478 0.1530 4700 4696 35.0 0.1430 0.1795 0.1430 4697 4696 31.7 0.1530 0.1878 0.1530 192 193 87.7 0.1711 1385085.9069 0.1360 193 194 122.8 0.6012 463629.3169 0.1000 4589 4585 98.8 0.1400 1434753.0952 0.1390 4586 4585 99.5 0.1525 1727093.0923 0.1520 4587 4586 91.3 0.1781 11019687.9112 0.1780 4588 4587 90.9 0.1780 7508588.7244 0.1780 4706 4588 96.7 0.1520 7576848.4015 0.1520 4591 4589 115.3 0.1401 374617.1180 0.1400 4590 4589 104.7 0.1231 385431.1813 0.1230 4593 4591 120.6 0.1482 84232.5460 0.1480 4592 4591 104.8 0.1001 97469.7963 0.1000 4598 4593 119.3 0.1520 34449.1440 0.1520 4594 4593 132.0 0.1391 34449.1610 0.1390 4596 4594 37.3 0.1401 0.2053 0.1400 4595 4594 38.0 0.1231 0.1829 0.1230 4599 4598 37.9 0.1780 0.2347 0.1780 4717 4715 42.7 0.1400 0.2049 0.1400 4716 4715 44.0 0.1000 0.1533 0.1000 4711 4709 107.3 0.1390 242148.6477 0.1390 4710 4709 105.7 0.1230 267458.4883 0.1230 4715 4711 114.1 0.1480 100450.2642 0.1480 4712 4711 122.6 0.1530 100450.2539 0.1530 4714 4712 44.6 0.1530 0.2242 0.1530 4713 4712 43.2 0.1530 0.2226 0.1530 step 1: Water molecule starting at atom 41146 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault I have the following nvt.mdp title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 150000 ; 2 * 150000 = 300 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein DRG ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bond ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_DRG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed If I do the constraints = none then i get the following warning- The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Should I change the dt=0.002 to dt=0.00001? What else can I do? Thanking you, Regards, Gaurav. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.