[gmx-users] segmantation default
mehmet kıytak
mehmetkiytak at gmail.com
Wed Feb 1 17:41:34 CET 2012
hi all...
ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı
use below mdp file
; Run control
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.002
nsteps = 50000 ; 100 ps
nstcomm = 100
; Output control
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 0
xtc-precision = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.5
[ Read 70 lines ]
^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos
^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell
GNU nano 2.2.2 File:
nvt.mdp
; Run control
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.002
nsteps = 50000 ; 100 ps
nstcomm = 100
; Output control
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 0
xtc-precision = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.5
[ Read 70 lines ]
^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos
^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell
GNU nano 2.2.2 File:
nvt.mdp
couple-lambda0 = vdw ; only van der Waals interactions
couple-lambda1 = none ; turn off everything, in this case
only vdW
couple-intramol = no
nstdhdl = 10
; Generate velocities to start
gen_vel = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
and ı received this message..
bombardment on your system
Getting Loaded...
Reading file nvt.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads
Loaded with Money
Making 2D domain decomposition 4 x 2 x 1
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.900710, max 1.180984 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 44.9 0.1000 0.0977 0.1000
1 3 90.0 0.1000 0.2019 0.1000
1 4 90.0 0.1000 0.2181 0.1000
Wrote pdb files with previous and current coordinates
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.900025, max 1.179635 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 44.9 0.1000 0.0977 0.1000
1 3 90.0 0.1000 0.2019 0.1000
1 4 90.0 0.1000 0.2180 0.1000
Back Off! I just backed up step0b_n4.pdb to ./#step0b_n4.pdb.1#
Back Off! I just backed up step0c_n4.pdb to ./#step0c_n4.pdb.1#
Wrote pdb files with previous and current coordinates
step 0
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.078096, max 0.132700 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 3 47.2 0.2019 0.0981 0.1000
1 4 90.0 0.2180 0.1133 0.1000
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.078081, max 0.132660 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 3 47.3 0.2019 0.0981 0.1000
1 4 90.0 0.2180 0.1133 0.1000
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.319803, max 2.026278 (between atoms 1 and 4)
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.349996, max 0.441907 (between atoms 11 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 65.3 0.0982 0.1006 0.1000
9 10 90.0 0.1090 0.1542 0.1090
1 3 90.0 0.0981 0.2058 0.1000
11 12 90.0 0.1090 0.1572 0.1090
1 4 90.0 0.1133 0.3026 0.1000
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.349913, max 0.441867 (between atoms 11 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9 10 90.0 0.1090 0.1542 0.1090
11 12 90.0 0.1090 0.1572 0.1090
Wrote pdb files with previous and current coordinates
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.320270, max 2.027545 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 65.3 0.0982 0.1006 0.1000
1 3 90.0 0.0981 0.2058 0.1000
1 4 90.0 0.1133 0.3028 0.1000
Back Off! I just backed up step2b_n4.pdb to ./#step2b_n4.pdb.1#
Back Off! I just backed up step2c_n4.pdb to ./#step2c_n4.pdb.1#
Wrote pdb files with previous and current coordinates
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 29.207302, max 49.092598 (between atoms 9 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.337072, max 0.559348 (between atoms 1 and 4)
step 3: Water molecule starting at atom 3147 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9 10 90.0 0.1542 5.4601 0.1090
1 2 90.0 0.1006 0.1091 0.1000
11 12 90.0 0.1572 1.4400 0.1090
1 3 90.0 0.2058 0.1140 0.1000
1 4 90.0 0.3028 0.1559 0.1000
Wrote pdb files with previous and current coordinates
step 3: Water molecule starting at atom 3147 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step3b_n2.pdb to ./#step3b_n2.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 29.207168, max 49.092289 (between atoms 9 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9 10 90.0 0.1542 5.4601 0.1090
11 12 90.0 0.1572 1.4401 0.1090
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.337002, max 0.559171 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 90.0 0.1006 0.1091 0.1000
1 3 90.0 0.2058 0.1141 0.1000
1 4 90.0 0.3028 0.1559 0.1000
Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1#
Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1#
Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1#
Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1#
Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
mkiytak at babil:~
PLEASE HELP ME...
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