Hi,
I have the following error when running energy minimization
(integrator=steep):
(similar message occurs serveral times in previous steps as for Step 57)
... ... ... ...
Step 57, time 0.114 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 110.960770 (between atoms 1576 and 1578) rms 1.979457
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1570 1572 34.5 0.1461 0.0907 0.1470
1571 1572 42.1 0.1396 0.0753 0.1470
1573 1574 69.9 0.0647 1.4014 0.1530
1574 1575 131.1 1.6322 4.1748 0.1430
1575 1576 174.5 1.6463 17.0315 0.1610
1576 1577 176.0 1.8019 16.5694 0.1480
1576 1578 176.1 1.7902 16.5702 0.1480
1576 1579 175.4 2.3035 17.5056 0.1610
1579 1580 156.6 2.7280 5.5397 0.1430
1580 1581 172.8 0.9601 1.8503 0.1530
1581 1582 40.2 0.0690 0.3042 0.1435
1581 1600 82.5 0.1137 0.2378 0.1530
Back Off! I just backed up step56.pdb to ./#step56.pdb.3#
Back Off! I just backed up step57.pdb to ./#step57.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 57, Dmax= 4.3e-03 nm, Epot= -1.79963e+23 Fmax= inf, atom= 2
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 5700 ]
Please report this to the mailing list (gmx-users@gromacs.org)
-------------------------------------------------------
I'd like to know if there is any method to let this EM run.
Thanks,
George
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