GROMACS version: gmx, version 2018.1
GROMACS modification: No
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Dear all, I am trying to simulate an revere micellar system, using GROMACS. I used CHARMM ff. During Mdrun, in NVT, the jobis getting terminated by following error:
Step 58549, time 58.549 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 3.250535, max 436.089630 (between atoms 4457 and 4453)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4454 4453 76.8 0.1339 1.6622 0.1337
4453 4458 99.5 0.1295 0.6384 0.1337
4458 4463 46.1 0.1495 0.3319 0.1483
4463 4464 57.4 0.1094 0.1917 0.1100
4463 4465 67.4 0.1097 0.2224 0.1100
4463 4466 62.1 0.1524 0.2952 0.1530
4466 4467 33.3 0.1102 0.1205 0.1100
4466 4468 37.8 0.1101 0.1303 0.1100
4466 4469 30.3 0.1533 0.1719 0.1530
4456 4452 90.1 0.1506 0.6091 0.1080
4452 4458 92.5 0.1394 0.6490 0.1370
4459 4454 83.9 0.1464 1.3864 0.1470
4452 4451 91.5 0.1358 1.8022 0.1370
4454 4451 85.3 0.1408 1.6710 0.1370
4455 4451 89.4 0.2011 1.9289 0.1080
4460 4459 114.7 0.1097 0.2535 0.1090
4461 4459 100.3 0.1097 0.3348 0.1090
4462 4459 86.9 0.1101 0.3523 0.1090
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
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Program: gmx mdrun, version 2018.1
Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282)
MPI rank: 6 (out of 8)
Fatal error:
1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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I minimized the system three times with different different forces (though the F max was E3, while I set it to 10). I have also used Berendsen thermostat during the NVT simulation. So, what may be the possible reasons and how can I solve it? As I read earlier replies, the primary reasons for such errors are mentioned to the geometry problem. I uploaded the parameter file here.
Thanks
Have you visualized the trajectory and checked the behavior of atoms ID 4457 and 4453?
Nebojša Zec
, I am sorry to see your reply and many thanks for giving time. Surely, I don't want that and the problem was still there after I corrected it. Then I specified number of GPUs for calculation and the system ran well. Previous it engaged all 4 GPUs. So that may be a way but I am not sure about it.- Badges
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