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 <[EMAIL PROTECTED]> 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
_________________________________________________________________
Dave vs. Carl: The Insignificant Championship Series. Who will win?
http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/?href=http://davevscarl.spaces.live.com/?icid=T001MSN38C07001
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
