[gmx-users] LINCS warning

[jayant james]

Hi!
I am getting a message in the MD log file as below with respect ro LINCS
mentioning deviations. I have constrained all bonds but this problem seems
to pertain to a water molecule. Please suggest a way to oversome this issue.
Thanks
Jayant James

Initializing LINear Constraint Solver

number of constraints is 4539

average number of constraints coupled to one constraint is 2.9

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.048807 517 518 0.006284

After LINCS 0.000551 520 522 0.000113

Going to use C-settle (72211 waters)

wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074

rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.064202 1746 1747 0.008456

After LINCS 0.000134 2867 2869 0.000018

Started mdrun on node 0 Fri Jan 9 12:43:22 2009

Initial temperature: 299.944 K

Step Time Lambda

0 0.00000 0.00000

Grid: 13 x 20 x 22 cells

Configuring nonbonded kernels...

Testing x86_64 SSE support... present.



Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.015569 675 676 0.001354

After LINCS 0.000080 520 522 0.000014

Energies (kJ/mol)

G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14

2.96794e+03 2.64964e+03 9.36791e+02 1.39165e+03 4.77210e+04

LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest.

6.48697e+05 -9.38928e+03 -4.00822e+06 -4.30837e+05 2.74831e+03

D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature

1.27022e+01 -3.74134e+06 5.53033e+05 -3.18830e+06 2.99966e+02

Pressure (bar)

-2.82027e+03

Grid: 13 x 21 x 22 cells

Grid: 13 x 21 x 23 cells

Grid: 13 x 21 x 22 cells

Grid: 13 x 21 x 23 cells

Grid: 13 x 21 x 22 cells

Grid: 13 x 21 x 23 cells

Step Time Lambda

5000 5.00000 0.00000

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.014423 4388 4389 0.001377

After LINCS 0.000026 3409 3410 0.000006

Energies (kJ/mol)

G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14

7.22704e+03 3.55030e+03 2.16248e+03 1.62198e+03 4.75481e+04

LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest.

5.11526e+05 -9.27329e+03 -3.36888e+06 -4.42423e+05 3.30945e+02

D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature

4.61447e+00 -3.24661e+06 5.52683e+05 -2.69393e+06 2.99776e+02

Pressure (bar)

2.28435e+01

Grid: 13 x 21 x 22 cells

Grid: 13 x 21 x 23 cells

Step Time Lambda

10000 10.00000 0.00000

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.016397 3336 3337 0.001453

After LINCS 0.000025 2689 2691 0.000006

Energies (kJ/mol)

G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14

7.09757e+03 3.64033e+03 2.11140e+03 1.63821e+03 4.76074e+04

LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest.

5.13273e+05 -9.28148e+03 -3.37251e+06 -4.42402e+05 2.78608e+02

D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature

4.20109e+00 -3.24855e+06 5.53775e+05 -2.69477e+06 3.00369e+02

Pressure (bar)

1.19419e+02

Grid: 13 x 21 x 22 cells

Grid: 13 x 21 x 23 cells

Step Time Lambda

15000 15.00000 0.00000

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.016405 2451 2452 0.001466

After LINCS 0.000030 520 522 0.000006

-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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