[gmx-users] LINCS warning
Justin Lemkul
jalemkul at vt.edu
Mon Apr 28 12:23:34 CEST 2014
On 4/28/14, 1:37 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
> 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
If the run crashes at step zero, it suggests a catastrophic failure, i.e. the
input configuration is not stable enough to simulate or there is a topology problem.
> 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?
I doubt it will help. If you want dt = 0.002, you must use constraints, so
turning them off is not a wise idea. The constraints are failing in the
simulation, but that doesn't mean they are the cause of the problem. They're
just the first thing to fail due to insanely high forces. Your run will
undoubtedly fail without constraints eventually.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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