<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks Justin,<br> now i have different problem when i run mdrun_d programme with the following command <br> ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr -c 1HHO_md.gro -e md.edr -nt 1<br>i got error as follows<br><span style="font-weight: bold;">Step 0, time 0 (ps) LINCS WARNING</span><br style="font-weight: bold;"><span style="font-weight: bold;">relative constraint deviation after LINCS:</span><br style="font-weight: bold;"><span style="font-weight: bold;">rms 0.348354, max 2.293388 (between atoms 27 and 28)</span><br style="font-weight: bold;"><span style="font-weight: bold;">bonds that rotated more than 30 degrees:</span><br style="font-weight: bold;"><span style="font-weight: bold;"> atom 1 atom 2 angle
previous, current, constraint length</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 45 47 30.1 0.1250 0.0966 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 45 46 89.4 0.1250 0.1611 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 44 45 38.0 0.1530 0.1715 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 36 37 89.8 0.1090 0.1977 0.1090</span><br style="font-weight:
bold;"><span style="font-weight: bold;"> 27 28 89.6 0.1090 0.3590 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 18 19 89.1 0.1090 0.1375 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 15 17 56.1 0.1250 0.1306 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 6 7 89.2 0.1090 0.1781 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;">Wrote pdb files with
previous and current coordinates</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;">Step 1, time 0.002 (ps) LINCS WARNING</span><br style="font-weight: bold;"><span style="font-weight: bold;">relative constraint deviation after LINCS:</span><br style="font-weight: bold;"><span style="font-weight: bold;">rms 6.925181, max 29.122365 (between atoms 9 and 10)</span><br style="font-weight: bold;"><span style="font-weight: bold;">bonds that rotated more than 30 degrees:</span><br style="font-weight: bold;"><span style="font-weight: bold;"> atom 1 atom 2 angle previous, current, constraint length</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 45 47 95.4 0.0966 0.1734 0.1250</span><br style="font-weight: bold;"><span style="font-weight:
bold;"> 36 37 90.1 0.1977 1.6174 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 27 28 90.1 0.3590 0.1991 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 18 20 61.3 0.1422 0.0426 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 18 19 91.3 0.1375 0.2554 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 15 17
89.4 0.1306 0.1306 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 11 18 86.8 0.1423 0.2272 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 10 12 90.0 0.1542 4.1927 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 10 11 89.4 0.1418 4.2147 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 9 13 36.9 0.1545
0.2135 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 9 10 89.3 0.1415 4.2171 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 8 9 39.6 0.1422 0.1957 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 6 7 89.3 0.1781 0.2107 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 2 11 87.7 0.1404 0.2813
0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;">Wrote pdb files with previous and current coordinates</span><br style="font-weight: bold;"><span style="font-weight: bold;">Warning: 1-4 interaction between 10 and 14 at distance 4.309 which is larger than the 1-4 table size 2.400 nm</span><br style="font-weight: bold;"><span style="font-weight: bold;">These are ignored for the rest of the simulation</span><br style="font-weight: bold;"><span style="font-weight: bold;">This usually means your system is exploding,</span><br style="font-weight: bold;"><span style="font-weight: bold;">if not, you should increase table-extension in your mdp file</span><br style="font-weight: bold;"><span style="font-weight: bold;">or with user tables increase the table size</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;">Step 2, time 0.004 (ps) LINCS WARNING</span><br style="font-weight:
bold;"><span style="font-weight: bold;">relative constraint deviation after LINCS:</span><br style="font-weight: bold;"><span style="font-weight: bold;">rms 1141861312104.288574, max 8387384410969.760742 (between atoms 36 and 37)</span><br style="font-weight: bold;"><span style="font-weight: bold;">bonds that rotated more than 30 degrees:</span><br style="font-weight: bold;"><span style="font-weight: bold;"> atom 1 atom 2 angle previous, current, constraint length</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 1 2 114.2 0.2088 307491611.7030 0.2000</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 44 45 41.6 0.1457 0.1972 0.1530</span><br style="font-weight:
bold;"><span style="font-weight: bold;"> 43 44 129.5 0.1536 16995520.2978 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 40 43 100.2 0.1544 526802811.8353 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 40 41 115.4 0.1427 1126735523.3763 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 39 42 110.6 0.1546 3296841333.8448 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 39 40
95.3 0.1427 3867105914.6031 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 38 39 103.0 0.1432 6773859895.7491 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 36 38 97.4 0.1419 20921022161.9095 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 36 37 89.9 1.6174 914224900795.8143 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 34 35 105.4 0.1340 772011346.9170 0.1340</span><br
style="font-weight: bold;"><span style="font-weight: bold;"> 32 36 97.9 0.1434 21005542749.8526 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 31 34 103.2 0.1533 4047716956.2246 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 31 32 100.6 0.1407 6865225352.3692 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 30 33 108.3 0.1530 640798229.9764 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;">
30 31 99.0 0.1401 4174186935.5429 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 29 30 120.6 0.1399 992312479.3422 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 27 29 111.0 0.1429 1205532064.0067 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 27 28 121.7 0.1991 412296837.5467 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 25 26 78.4 0.1354
5.1420 0.1340</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 23 27 97.8 0.1457 412296831.0029 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 22 25 106.1 0.1565 14.5779 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 22 23 81.6 0.1448 15.7238 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 21 24 98.1 0.1614 4.0101 0.1530</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 21 22 88.5 0.1472 15.3081 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 20 21 95.2 0.1568 14.5247 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 18 20 84.5 0.0426 15.1546 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 18 19 90.3 0.2554 3.8535 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 15
17 89.9 0.1306 4.2160 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 15 16 90.0 0.1191 25.1978 0.1250</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 14 15 88.7 0.1553 3.4423 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 13 14 97.9 0.1679 2.7244 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 11 18 76.7 0.2272
23.5748 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 10 12 170.5 4.1927 15.3594 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 10 11 126.4 4.2147 26.6521 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 9 13 51.9 0.2135 3.3106 0.1530</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 9 10 165.5 4.2171 16.1115 0.1400</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 8 9 76.6 0.1957 7.1674 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 6 41 109.4 0.1477 1166436972.1222 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 6 8 117.5 0.1602 406664611.1456 0.1400</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 6 7 135.7 0.2107 406664648.5804 0.1090</span><br style="font-weight: bold;"><span style="font-weight: bold;">
5 41 115.5 0.1408 3655729543.2299 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 5 38 106.1 0.1421 6636732910.3252 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4 32 105.3 0.1409 6209428864.9749 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4 29 114.0 0.1420 4072911915.0192 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 3 23 112.7 0.1483
125990964.2723 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 3 20 130.8 0.1584 125990986.2569 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 2 11 45.9 0.2813 96334844.6580 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 2 8 153.6 0.1399 96334840.9361 0.1380</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 1 5 101.1 0.1999 3861844055.9208 0.2000</span><br
style="font-weight: bold;"><span style="font-weight: bold;"> 1 4 99.4 0.2050 4350154899.2293 0.2000</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 1 3 120.9 0.2049 276545143.5239 0.2000</span><br style="font-weight: bold;"><span style="font-weight: bold;">Wrote pdb files with previous and current coordinates</span><br style="font-weight: bold;"><span style="font-weight: bold;">Segmentation fault</span><br style="font-weight: bold;"><br><span style="background-color: rgb(255, 255, 0);">i am using the following .mdp files</span><br style="background-color: rgb(255, 255, 0);"><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255,
0);">title = Umbrella pulling simulation </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">define = -DPOSRES</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Run parameters</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">integrator = md</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">dt = 0.002</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">tinit = 0</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nsteps = 50000 ;
500 ps</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstcomm = 10</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Output parameters</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstxout = 5000 ; every 10 ps</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstvout = 5000 </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstfout = 500</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstxtcout = 500 ; every 1 ps</span><br style="background-color:
rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstenergy = 500</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Bond parameters</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">constraint_algorithm = lincs</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">constraints = all-bonds</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">continuation = no ; continuing from NPT </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Single-range cutoff scheme</span><br
style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">nstlist = 5</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">ns_type = grid </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">rlist = 0.9</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">rcoulomb = 0.9</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">rvdw = 1.4</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; PME electrostatics parameters</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255,
0);">coulombtype = PME</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">fourierspacing = 0.12</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">fourier_nx = 0</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">fourier_ny = 0</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">fourier_nz = 0</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pme_order = 3</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">ewald_rtol = 1e-5</span><br style="background-color:
rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">optimize_fft = yes</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Berendsen temperature coupling is on in two groups</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">Tcoupl = V-rescale </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">tc-grps = HEM AL OXY ; two coupling groups - more accurate</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">tau_t = 0.1 0.1 0.1 ; time constant, in ps</span><br style="background-color: rgb(255, 255, 0);"><span
style="background-color: rgb(255, 255, 0);">ref_t = 310 310 310 </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Pressure coupling is on</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">;Pcoupl = Parrinello-Rahman </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">;pcoupltype = isotropic</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">;tau_p = 1.0 </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">;compressibility =
4.5e-5</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">;ref_p = 1.0</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Generate velocities is off</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">gen_vel = no </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Periodic boundary conditions are on in all directions</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pbc = xyz</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Long-range dispersion correction</span><br style="background-color: rgb(255, 255, 0);"><span
style="background-color: rgb(255, 255, 0);">DispCorr = EnerPres</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">; Pull code</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull = umbrella</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_geometry = distance</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_dim = N Y N</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_start = yes ; define initial COM distance > 0</span><br style="background-color: rgb(255, 255,
0);"><span style="background-color: rgb(255, 255, 0);">pull_ngroups = 1</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_group0 = Fe </span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_group1 = O1</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">pull_k1 = 1000 ; kJ mol^-1 nm^-2</span><br style="background-color: rgb(255, 255, 0);"><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">I am
expecting your reply</span><br style="background-color: rgb(255, 255, 0);"><span style="background-color: rgb(255, 255, 0);">thanks in advance</span><br style="background-color: rgb(255, 255, 0);"><br></td></tr></table>