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@babil:~ PLEASE HELP ME...
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