[gmx-users] Segmentation fault 3
Tanos C. C. França
tccf at epq.ime.eb.br
Fri Mar 28 01:04:01 CET 2003
Hi folks,
I am facing the problem of segmentation fault again
!!!!!!!!!!!! This time I am trying to perform a Position Restrained (PR)
molecular dynamics (MD) of a crystallographic structure I have used
before to build a model by homology. I used the same parameters as to
the model but the calculation did not go on. With the model everything
went fine. I have performed 10 ps of PR MD and latter 100 ps of MD but
with the crystal structure nothing seems to work !!!!!!!!!!!!! I am
sending below the tail of my prlog.log file and my pr.mdp file.
Thanks a lot in advance if someone could help me.
Best
Tanos C. C. Franca.
TAIL OF PRLOG.LOG
Step 114, time 0.114 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2.016897 (between atoms 716 and 717) rms 0.020721
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
716 717 90.1 0.7000 0.3258 0.1080
Constraint error in algorithm Lincs at step 114
Step 115, time 0.115 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 13639.835303 (between atoms 716 and 717) rms 140.494485
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
696 709 37.7 0.1535 0.2057 0.1530
709 710 37.9 0.1229 0.1467 0.1230
709 711 154.9 0.1334 0.1971 0.1330
711 712 117.4 0.1001 0.2346 0.1000
711 713 87.3 0.1472 0.6345 0.1470
713 714 97.3 0.1533 8.4348 0.1530
713 727 88.6 0.1532 0.6032 0.1530
714 715 83.9 0.1556 10.5211 0.1530
715 716 99.0 0.1435 30.3582 0.1390
715 718 87.6 0.1419 23.3350 0.1390
716 717 90.0 0.3258 1473.2102 0.1080
716 720 94.1 0.1368 47.1645 0.1390
718 719 90.9 0.1098 20.1598 0.1080
718 722 91.7 0.1410 72.4517 0.1390
720 721 106.7 0.1077 9.1440 0.1080
720 724 93.5 0.1393 39.6938 0.1390
722 723 91.3 0.1082 56.1046 0.1080
722 724 93.0 0.1389 36.3105 0.1390
724 725 93.9 0.1356 47.1834 0.1360
725 726 90.3 0.1001 17.8042 0.1000
727 728 132.9 0.1231 0.2556 0.1230
727 729 117.0 0.1331 0.2292 0.1330
729 730 38.4 0.1000 0.1370 0.1000
729 731 36.2 0.1470 0.1925 0.1470
Constraint error in algorithm Lincs at step 115
MY PR.MDP FILE
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
title = PEP MD
cpp = /lib/cpp
define = -DPOSRE
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 10000 ; total 10ps
nstcomm = 1
nstxout = 100
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = Berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein plp ffo sol Na
ref_t = 300 300 300 300 300
; Pressure coupling is not on
Pcoupl = no
pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is on at 300 K
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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