[gmx-users] reg lincs error and exploding problem during mdrun
vidhya sankar
scvsankar_agr at yahoo.com
Mon May 2 06:33:16 CEST 2011
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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