<br>
hello users,<br>
<br>
i am using gromacs 3.3 version on unix platform<br>
i got these error while running MD simulation of 89 aa in spc216 water
for 10ns at step 4088373 time 8176.55 .i had used force field
4a1(official distribution)<br>
hear I'm sending .mdp file also<br>
error which i got is <br>
<span style="font-family: monospace;"><br>
------------------------------------------------------------------------------------------------------------------<br>
</span>step 4088520, will finish at Sat Sep 22 06:22:35 2007<br>
<br>
Step 4088530, time 8177.06 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 17.051964 (between atoms 615 and 616) rms 0.709711<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
613 614
35.7 0.1233
0.1232 0.1230<br>
613 615
35.2 0.1332
0.1352 0.1330<br>
615 616
90.0 0.0997
1.8052 0.1000<br>
615 617
90.0 0.1322
1.3965 0.1000<br>
step 4088530, will finish at Sat Sep 22 06:22:35 2007Warning: 1-4 interaction at<br>
distance larger than 1<br>
These are ignored for the rest of the simulation<br>
turn on -debug for more information<br>
<br>
Step 4088531, time 8177.06 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 1.625723 (between atoms 615 and 617) rms 0.062578<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
612 613
46.4 0.1548
0.1344 0.1530<br>
613 614
37.2 0.1232
0.1816 0.1230<br>
613 615
89.7 0.1352
0.2216 0.1330<br>
615 616
76.3 1.8052
0.1476 0.1000<br>
615 617
89.7 1.3965
0.2626 0.1000<br>
<br>
Step 4088532, time 8177.06 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 14.399930 (between atoms 615 and 616) rms 0.598937<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
611 612
44.2 0.1693
0.1761 0.1530<br>
612 613
35.4 0.1344
0.1669 0.1530<br>
613 614
95.7 0.1816
0.1308 0.1230<br>
615 616
90.2 0.1476
1.5400 0.1000<br>
615 617
90.5 0.2626
1.1927 0.1000<br>
<br>
Step 4088533, time 8177.07 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 1.051080 (between atoms 615 and 617) rms 0.046065<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
609 611
44.5 0.1529
0.1910 0.1470<br>
611 612
39.9 0.1761
0.1800 0.1530<br>
611 618
41.9 0.1579
0.1736 0.1530<br>
612 613
105.9 0.1669
0.2124 0.1530<br>
613 614
123.8 0.1308
0.1181 0.1230<br>
613 615
34.6 0.1178
0.2224 0.1330<br>
615 616
74.0 1.5400
0.1253 0.1000<br>
615 617
80.3 1.1927
0.2051 0.1000<br>
<br>
Step 4088534, time 8177.07 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 45040.144531 (between atoms 613 and 614) rms 1994.670654<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
582 584
41.9 0.1470
0.2116 0.1470<br>
584 585
41.3 0.1530
0.2102 0.1530<br>
584 586
69.2 0.1530
8.3830 0.1530<br>
586 587
59.2 0.1230
8.3382 0.1230<br>
586 588
78.9 0.1331
28.5889 0.1330<br>
588 589
75.7 0.1001
27.4635 0.1000<br>
588 590
80.7 0.1471 156.4029
0.1470<br>
590 591
82.5 0.1531 156.2125
0.1530<br>
590 607
84.1 0.1537 272.5951
0.1530<br>
591 592
78.3 0.1531
23.8232 0.1530<br>
592 593
55.2 0.1330
6.7518 0.1330<br>
592 595
55.7 0.1390
6.7401 0.1390<br>
593 594
41.6 0.1090
0.1595 0.1090<br>
593 596
45.1 0.1330
0.1971 0.1330<br>
595 598
37.7 0.1390
0.1911 0.1390<br>
595 599
34.4 0.1390
0.1923 0.1390<br>
607 608
85.1 0.1235 322.3230
0.1230<br>
607 609
90.8 0.1334 722.2238
0.1330<br>
609 610
87.5 0.1001 730.5731
0.1000<br>
609 611
91.7 0.1910 2220.5916
0.1470<br>
611 612 113.1 0.1800 1928.0201 0.1530<br>
611 618
61.9 0.1736 2612.3730
0.1530<br>
612 613 152.6 0.2124 2170.9067 0.1530<br>
613 614
95.0 0.1181 5540.0610
0.1230<br>
613 615 100.8 0.2224 1264.8948 0.1330<br>
615 616
88.0 0.1253 729.0342
0.1000<br>
615 617
69.1 0.2051 610.1647
0.1000<br>
618 619
96.0 0.1365 1772.1053
0.1230<br>
618 620 101.8 0.1456 1954.0292 0.1330<br>
620 621
97.1 0.1014 161.6277
0.1000<br>
620 622
44.0 0.1484 387.2649
0.1470<br>
622 623 119.2 0.1536 271.5126 0.1530<br>
622 628 110.2 0.1536 303.3078 0.1530<br>
623 624
65.6 0.1531
51.2406 0.1530<br>
624 625
113.7 0.1530
26.6845 0.1530<br>
625 626
32.7 0.1250
0.1557 0.1250<br>
625 627
34.2 0.1250
0.1577 0.1250<br>
628 629
78.5 0.1232
35.4732 0.1230<br>
628 630
106.0 0.1331
32.5768 0.1330<br>
630 631
111.3 0.1000
10.4951 0.1000<br>
630 632
136.9 0.1471
10.4534 0.1470<br>
632 633
34.5 0.1530
0.1991 0.1530<br>
632 637
34.5 0.1530
0.2035 0.1530<br>
Fatal error: Determinant = 25363147356027562275897344.000000<br>
--------------------------------------------------------------------------------------------------<br>
hear it is telling that bonds are rotating more than 30 degrees
and showing LINCS error with respect to the relative constraint
deviation and <br>
in some cases atom -1, atom-2 current value is much high compare to
previous and determinent is also too high .is i need to keep any bond
constriants? ,what is the reason for these error<br>
what changes should i do in my .mdp file so that i can over come these problems<br>
<br>
Hear my .mdp file<br>
-----------------------<br>
;<br>
; User spoel (236)<br>
; Wed Nov 3 17:12:44 1993<br>
; Input file<br>
;<br>
title = Yo<br>
cpp = /lib/cpp<br>
constraints = all-bonds<br>
;define = -DPOSRES -DPOSRES_WATER<br>
integrator = md<br>
comm_mode = Angular<br>
dt
= 0.002 ; ps !<br>
nsteps = 5000000 ; total 10000 ps.<br>
nstcomm = 1<br>
nstxout = 500<br>
nstvout = 500<br>
nstfout = 500<br>
nstlog = 500<br>
nstenergy = 500<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 0.9<br>
rcoulomb = 0.9<br>
rvdw = 0.9<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc-grps = Protein SOL NA+<br>
tau_t
= 0.1
0.1 0.1<br>
ref_t
= 300
300 300<br>
; Energy monitoring<br>
energygrps = Protein<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = no<br>
Pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is off at 300 K.<br>
gen_vel = no<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
--------------------------<br>
regards <br>
vijay kumar<br>
<br>
<br>
<br>
<br>