[gmx-users] LINCS error
vijay kumar hinge vijay
vijaybioinfo2 at gmail.com
Mon Sep 17 12:22:21 CEST 2007
hello users,
i am using gromacs 3.3 version on unix platform
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)
hear I'm sending .mdp file also
error which i got is
------------------------------------------------------------------------------------------------------------------
step 4088520, will finish at Sat Sep 22 06:22:35 2007
Step 4088530, time 8177.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 17.051964 (between atoms 615 and 616) rms 0.709711
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
613 614 35.7 0.1233 0.1232 0.1230
613 615 35.2 0.1332 0.1352 0.1330
615 616 90.0 0.0997 1.8052 0.1000
615 617 90.0 0.1322 1.3965 0.1000
step 4088530, will finish at Sat Sep 22 06:22:35 2007Warning: 1-4
interaction at
distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information
Step 4088531, time 8177.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1.625723 (between atoms 615 and 617) rms 0.062578
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
612 613 46.4 0.1548 0.1344 0.1530
613 614 37.2 0.1232 0.1816 0.1230
613 615 89.7 0.1352 0.2216 0.1330
615 616 76.3 1.8052 0.1476 0.1000
615 617 89.7 1.3965 0.2626 0.1000
Step 4088532, time 8177.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 14.399930 (between atoms 615 and 616) rms 0.598937
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
611 612 44.2 0.1693 0.1761 0.1530
612 613 35.4 0.1344 0.1669 0.1530
613 614 95.7 0.1816 0.1308 0.1230
615 616 90.2 0.1476 1.5400 0.1000
615 617 90.5 0.2626 1.1927 0.1000
Step 4088533, time 8177.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1.051080 (between atoms 615 and 617) rms 0.046065
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
609 611 44.5 0.1529 0.1910 0.1470
611 612 39.9 0.1761 0.1800 0.1530
611 618 41.9 0.1579 0.1736 0.1530
612 613 105.9 0.1669 0.2124 0.1530
613 614 123.8 0.1308 0.1181 0.1230
613 615 34.6 0.1178 0.2224 0.1330
615 616 74.0 1.5400 0.1253 0.1000
615 617 80.3 1.1927 0.2051 0.1000
Step 4088534, time 8177.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 45040.144531 (between atoms 613 and 614) rms 1994.670654
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
582 584 41.9 0.1470 0.2116 0.1470
584 585 41.3 0.1530 0.2102 0.1530
584 586 69.2 0.1530 8.3830 0.1530
586 587 59.2 0.1230 8.3382 0.1230
586 588 78.9 0.1331 28.5889 0.1330
588 589 75.7 0.1001 27.4635 0.1000
588 590 80.7 0.1471 156.4029 0.1470
590 591 82.5 0.1531 156.2125 0.1530
590 607 84.1 0.1537 272.5951 0.1530
591 592 78.3 0.1531 23.8232 0.1530
592 593 55.2 0.1330 6.7518 0.1330
592 595 55.7 0.1390 6.7401 0.1390
593 594 41.6 0.1090 0.1595 0.1090
593 596 45.1 0.1330 0.1971 0.1330
595 598 37.7 0.1390 0.1911 0.1390
595 599 34.4 0.1390 0.1923 0.1390
607 608 85.1 0.1235 322.3230 0.1230
607 609 90.8 0.1334 722.2238 0.1330
609 610 87.5 0.1001 730.5731 0.1000
609 611 91.7 0.1910 2220.5916 0.1470
611 612 113.1 0.1800 1928.0201 0.1530
611 618 61.9 0.1736 2612.3730 0.1530
612 613 152.6 0.2124 2170.9067 0.1530
613 614 95.0 0.1181 5540.0610 0.1230
613 615 100.8 0.2224 1264.8948 0.1330
615 616 88.0 0.1253 729.0342 0.1000
615 617 69.1 0.2051 610.1647 0.1000
618 619 96.0 0.1365 1772.1053 0.1230
618 620 101.8 0.1456 1954.0292 0.1330
620 621 97.1 0.1014 161.6277 0.1000
620 622 44.0 0.1484 387.2649 0.1470
622 623 119.2 0.1536 271.5126 0.1530
622 628 110.2 0.1536 303.3078 0.1530
623 624 65.6 0.1531 51.2406 0.1530
624 625 113.7 0.1530 26.6845 0.1530
625 626 32.7 0.1250 0.1557 0.1250
625 627 34.2 0.1250 0.1577 0.1250
628 629 78.5 0.1232 35.4732 0.1230
628 630 106.0 0.1331 32.5768 0.1330
630 631 111.3 0.1000 10.4951 0.1000
630 632 136.9 0.1471 10.4534 0.1470
632 633 34.5 0.1530 0.1991 0.1530
632 637 34.5 0.1530 0.2035 0.1530
Fatal error: Determinant = 25363147356027562275897344.000000
--------------------------------------------------------------------------------------------------
hear it is telling that bonds are rotating more than 30 degrees and showing
LINCS error with respect to the relative constraint deviation and
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
what changes should i do in my .mdp file so that i can over come these
problems
Hear my .mdp file
-----------------------
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
cpp = /lib/cpp
constraints = all-bonds
;define = -DPOSRES -DPOSRES_WATER
integrator = md
comm_mode = Angular
dt = 0.002 ; ps !
nsteps = 5000000 ; total 10000 ps.
nstcomm = 1
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
nstlist = 10
ns_type = grid
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL NA+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein
; Isotropic pressure coupling is now on
Pcoupl = no
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
--------------------------
regards
vijay kumar
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