[gmx-users] LINCS
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Wed Aug 26 20:36:45 CEST 2009
Hi Justin,
I tried to run full MD after energy minimization in both vacuo and
water... went good but I got this ERROR once I try to run full MD.
Can you please help.....
=============================================================
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.014761, max 0.067846 (between atoms 416 and 417)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'VioLanthrone in water'
50000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 336.210453, max 3218.528809 (between atoms 415 and 416)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
70 71 41.8 0.1530 0.2361 0.1530
69 70 121.0 0.1531 1.9697 0.1530
67 68 156.3 0.1624 8.0600 0.1530
66 67 64.6 0.1621 29.2909 0.1530
65 66 108.7 0.1578 35.0944 0.1530
64 65 72.8 0.1591 33.9603 0.1530
63 64 127.8 0.1603 5.8064 0.1530
61 62 131.8 0.1531 0.3537 0.1530
60 61 57.1 0.1530 0.1243 0.1530
286 285 38.1 0.1368 0.1513 0.1360
284 285 93.8 0.1385 0.3739 0.1360
283 284 91.3 0.1443 1.0202 0.1390
282 283 78.9 0.1452 7.6810 0.1390
281 282 80.3 0.1448 9.0651 0.1390
279 281 80.6 0.1446 3.3017 0.1390
279 280 139.2 0.1440 0.7653 0.1390
278 279 74.6 0.1430 11.7061 0.1390
278 277 88.7 0.1423 9.9988 0.1390
276 277 48.8 0.1410 1.5366 0.1390
275 276 90.1 0.1396 4.7914 0.1390
274 275 87.3 0.1405 18.6892 0.1390
273 278 86.5 0.1423 6.0358 0.1390
273 274 89.5 0.1413 19.8101 0.1390
271 273 74.4 0.1422 6.3080 0.1390
271 272 93.5 0.1258 8.1775 0.1230
270 281 68.1 0.1445 2.5745 0.1390
270 271 93.4 0.1431 8.6284 0.1390
270 269 71.4 0.1414 1.5530 0.1390
268 269 80.6 0.1406 6.4334 0.1390
267 282 67.5 0.1443 25.7157 0.1390
267 268 68.7 0.1427 28.0430 0.1390
266 267 86.1 0.1436 72.5722 0.1390
266 265 84.8 0.1422 222.9021 0.1390
264 265 90.4 0.1408 390.2640 0.1390
263 264 86.2 0.1415 393.1811 0.1390
261 263 96.6 0.1433 30.2353 0.1390
261 262 56.1 0.1257 22.0580 0.1230
260 261 60.5 0.1428 22.8828 0.1390
260 259 88.4 0.1411 1.0891 0.1390
257 258 114.8 0.1394 0.3860 0.1390
256 257 132.5 0.1399 0.2469 0.1390
255 260 78.1 0.1426 1.3243 0.1390
255 256 45.5 0.1414 0.7532 0.1390
253 263 65.5 0.1447 32.5754 0.1390
252 266 80.3 0.1448 71.8742 0.1390
252 253 64.6 0.1449 14.7647 0.1390
251 252 76.8 0.1449 18.2314 0.1390
254 250 65.1 0.1428 1.7857 0.1390
249 251 75.9 0.1440 2.1153 0.1390
249 250 53.4 0.1426 0.1141 0.1390
249 248 32.3 0.1388 0.1975 0.1360
438 437 37.1 0.1366 0.1946 0.1360
436 437 127.5 0.1377 2.6510 0.1360
434 435 66.8 0.1428 4.2026 0.1390
433 434 163.9 0.1415 2.0503 0.1390
436 432 123.3 0.1406 2.7198 0.1390
420 421 128.4 0.1398 2.1740 0.1390
419 434 48.9 0.1421 1.2412 0.1390
418 419 163.9 0.1432 18.4852 0.1390
418 417 52.7 0.1431 31.4670 0.1390
416 417 147.5 0.1484 136.8367 0.1390
415 416 58.2 0.1449 447.5145 0.1390
413 415 152.0 0.1475 331.5535 0.1390
413 414 56.7 0.1261 283.8908 0.1230
412 413 62.3 0.1446 272.3644 0.1390
412 411 168.8 0.1449 54.1788 0.1390
409 410 137.2 0.1402 4.5705 0.1390
408 409 65.3 0.1430 1.8876 0.1390
407 412 119.8 0.1459 25.1600 0.1390
407 408 85.4 0.1446 14.0232 0.1390
406 407 56.4 0.1469 17.4775 0.1390
405 415 63.3 0.1460 430.7261 0.1390
405 406 92.7 0.1471 85.9366 0.1390
404 418 61.0 0.1462 49.7659 0.1390
404 405 157.2 0.1470 116.1591 0.1390
403 435 139.3 0.1448 26.6457 0.1390
406 402 121.8 0.1454 5.0911 0.1390
401 403 98.2 0.1445 23.9140 0.1390
401 402 64.2 0.1449 0.5887 0.1390
401 400 117.1 0.1385 0.6435 0.1360
398 400 129.7 0.1371 0.6799 0.1360
398 399 32.1 0.1233 0.1598 0.1230
step 0Segmentation fault
===========================================================
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> Warren Gallin wrote:
>> Hi,
>>
>> I am trying to work my way through learning to use GROMACS 4.0.5
>> for doing MD simulations of short peptides in solution.
>>
>> My problem is that several peptides, most strikingly a Serine
>> 10-mer, are exploding during the production run.
>>
>> I construct the serine polymer in extended form using TINKER,
>> with neither end capped, then use pdb2gmx, editconv, genbox and
>> genion to set the forcefield to OPLSAA/L, place it in a box of
>> tip3p water, neutralized in a .096 M NaCl solution.
>>
>> I am trying to track down why this is occurring, and the first
>> thing that seems suspicious is that the initial energy minimization
>> run reaches convergence with a rather large force remaining on one
>> of the atoms - the final statement from the EM run is:
>>
>>
>> Steepest Descents converged to machine precision in 6793 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy = -4.9731194e+05
>> Maximum force = 7.1219537e+02 on atom 111
>> Norm of force = 6.5289087e+00
>>
>>
>> So I am thinking that with a large initial force on the polymer
>> the system might be unrecoverably unstable and this is propagating
>> through the subsequent steps of relaxing the water and the actual
>> MD run to pop up as an explosion.
>>
>> If I look at the run log for the MD run, everything seems stable
>> until the last step, at which point the temperature shoots up and
>> the serine polymer explodes. Here are the last four steps from the
>> run log:
>>
>> Step Time Lambda
>> 208200 416.40002 0.00000
>>
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>> 9.75158e+03 1.25586e+02 7.62176e+00 -6.45482e+01 1.16773e+02
>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>> 1.80001e+03 6.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05
>> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
>> 7.77043e+04 -3.15843e+05 1.01418e+06 3.17587e+02 -2.87690e+02
>>
>> Step Time Lambda
>> 208300 416.60002 0.00000
>>
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>> 1.04345e+04 1.96147e+02 1.55806e+01 -3.31126e+01 1.24787e+02
>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>> 1.80413e+03 6.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05
>> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
>> 7.77229e+04 -3.14815e+05 1.02114e+06 3.17663e+02 -2.94492e+02
>>
>> Step Time Lambda
>> 208400 416.80002 0.00000
>>
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>> 7.10106e+03 2.06975e+02 1.21357e+01 -2.52705e+01 1.16229e+02
>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>> 1.85247e+03 6.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05
>> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
>> 7.58806e+04 -3.19943e+05 1.02333e+06 3.10133e+02 -2.90942e+02
>>
>> Step Time Lambda
>> 208500 417.00002 0.00000
>>
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>> 2.30968e+04 4.27637e+02 1.17359e+01 -5.59373e+01 1.39477e+02
>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>> 1.80067e+03 6.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05
>> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
>> 1.03323e+05 -2.76511e+05 1.07569e+06 4.22292e+02 2.94766e+02
>>
>> So my questions are:
>>
>> 1) Am I missing some obvious step in setting up a stable simulation?
>
> You'll have to describe your equilibration protocol in detail,
> including your .mdp file, because energy minimization alone is not
> enough.
>
>> 2) Is it true that the high internal force present at the end of
>> the initial energy minimization could be the root of the problem?
>
> Possibly. However, I routinely minimize my protein structures to
> Fmax < 1000 (usually they reach about 700-900 Fmax), and I've not
> had a problem.
>
>> 3) If so, is there an obvious method for relaxing the system
>> into a more stable state prior to the main MD run?
>
> See my response to #1. Thorough equilibration is required, but we
> don't know all what you've done.
>
> -Justin
>
>>
>> Warren Gallin
>> _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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