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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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