[gmx-users] Crashes during protein-ligand simulation

James Starlight jmsstarlight at gmail.com
Fri Jul 6 07:12:45 CEST 2012

Dear Gromacs users!

I have some problems with the simulation of protein-ligand complex
embedded in the ccl4-water environment. In addition there are some
crystallography waters (xw) embedded in the protein interiour of the
protein. I've done equilibration and minimisation of my system and run
it in NVT ensemble.

Finally I've already simulated this system in the apo form as well as
without XW and there were no any problems.

In the current case my system always crashed after 10-15 ns of
simulation with the errors like

Step 6651310, time 13302.6 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.060675, max 1.520945 (between atoms 3132 and 3130)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3148   3147   90.0    0.1281   0.1483      0.1000
   3150   3149   90.0    0.1084   0.1444      0.1000
   3131   3130   90.0    0.1321   0.1325      0.1000
   3132   3130   90.0    0.1067   0.2521      0.1000

Program mdrun_mpi.openmpi, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189

here both atoms 3132 and 3130 are from LIGAND.

During data analysing I didnt observed any serious artifacts in that
system. In addition RMSD both of protein and ligand were very stable.
Finally there are no fluctuations in energy or temperature. So I could
understand why this crasshes could occur. If I try to continue this
simulation from the crasshed checkpoint my simulation always goon but
within next 5-10ns I've always obtain second crash etc.

This is the last step from log file

DD  step 6649999  vol min/aver 0.758  load imb.: force  1.0%  pme
mesh/force 0.708

           Step           Time         Lambda
        6650000    13300.00000        0.00000

   Energies (kJ/mol)
          Angle       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    5.78299e+01    1.24988e+04    2.10966e+03    1.81619e+03    8.94229e+01
     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
    4.65481e+04    8.27301e+04   -6.89535e+03   -2.15286e+03   -7.16722e+05
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
   -1.72813e+05   -7.52733e+05    1.46708e+05   -6.06025e+05   -1.37045e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.10968e+02   -9.74796e+01    2.52993e+02    1.55693e-05

Could you explain me what could be wrong with that system and what
addition data should I provide to help sheld light on that problem ?

Thanks for help


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