[gmx-users] Water molecule can not be settled

Wed Jan 17 15:32:56 CET 2007

Hi Sunny,

The problem here is not the water. You have some serious problems with
your starting structure (which I already suspected from your previous
mails). It looks like your system has been very busy exploding, but
you never noticed because of the l-bfgs algorithm (controlled
explosion). Notice that at step -2 (!!!) all your constraints are out
of bounds(except for those involving the solvent which you've added).
In other words, all constraints were out of bounds after energy
minimization. Probably your best chance is to start anew. Don't forget
to visually inspect your system after every step and check for
overlaps.

By the way, how did you put the protein in the bilayer? Did you
perform an energy minimization on the protein before that?

Tsjerk

On 1/17/07, Sunny <ge_sunny at hotmail.com> wrote:
> Hi,
>
> I have a structure with 1 protein (118 atoms), 256 DPPC lipids (12800
> atoms), and 3833 water molecules (11499 atoms). The box size is 6.125, 12.5,
> 9.5 nm.
>
> Water is add by genbox:    genbox -cp input.pdb -cs spc216.gro -vdwd 0.45 -o
> output.pdb
>
> After the water added, I run the l-bfgs energy minimization on it.
>
> Then I run md simulation (integrator=md, dt=0.002). The md simulation fails
> with a Segmentatin fault and the following message in md.log:
>
> Step -2, time -0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 9.488017 (between atoms 48 and 49) rms 0.158390
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>       1      5   30.2    0.0554   0.1507      0.1470
>       6      7   32.2    0.1284   0.1220      0.1230
>      ... ...
>   12896  12897   60.6    0.4879   0.2176      0.1530
>   12897  12898   55.7    0.2474   0.1692      0.1530
> Constraint error in algorithm Lincs at step -2
> Going to use C-settle (3833 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         9.488017     48     49   0.158390
>         After LINCS         50.828369     43     48   0.866281
>
> Step -1, time -0.0005 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 50.828369 (between atoms 43 and 48) rms 0.866281
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>      33     35   39.5    0.1502   0.1805      0.1470
>      35     36   40.8    0.1541   0.1945      0.1530
>      ... ...
>    5697   5698   69.7    0.1900   0.1719      0.1530
>    6865   6866   93.4    0.1876   0.1722      0.1530
> Constraint error in algorithm Lincs at step -1
> Started mdrun on node 0 Wed Jan 17 13:50:30 2007
> Initial temperature: 7.0078e+06 K
>            Step           Time         Lambda
>               0        0.00000        0.00000
>
> Grid: 12 x 25 x 19 cells
> Configuring nonbonded kernels...
>
> There are 24417 atoms in your xtc output selection
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         40346476102025216.000000   1367   1368
> 507031760928768.000000
>         After LINCS         39707178809950208.000000   1367   1368
> 484342119792640.000000
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 39707178809950208.000000 (between atoms 1367 and 1368) rms
> 484342119792640.000000
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>       1      2   91.8    0.0966 4259.4292      0.1000
>       1      3  113.4    0.0993 4259.4448      0.1000
>       ... ...
>   12897  12898   89.4    0.1692 5628.2495      0.1530
>   12898  12899   91.9    0.1592 438.1604      0.1530
> Constraint error in algorithm Lincs at step 0
>
> t = 0.000 ps: Water molecule starting at atom 15877 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> previous and current coordinates
> Large VCM(group rest): -50006056.00000, 291892.96875, 10607907.00000,
> ekin-cm:  3.37458e+20
>    Energies (kJ/mol)
>           Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
>     9.54095e+04    1.09247e+04    1.06727e+04    2.10367e+04    5.80276e+03
>           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
>     1.50514e+04    2.85987e+04    2.60953e+20   -1.27608e+05   -2.07571e+05
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>     2.60953e+20            INF            INF            INF            INF
>
> How can I fix this error?
>
> Thanks,
>
> Sunny
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623