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