[gmx-users] big protein dynamics

Adriana Pietropaolo adriana at ms.fci.unibo.it
Wed Nov 30 16:48:46 CET 2005

Thanks a lot for your help!
Now, I had been able to make a reasonable box with 26000 water molecules 
and my protein.
I used grompp and I processed the topology file with 4 tasks.
When I run MD simulation, constraining all bonds to equilibrate my water 
molecules there's this error:
Constraint error in algorithm Lincs at step 0
   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    6.38409e+03    2.55973e+02    4.45790e+03    5.51719e+03    2.38409e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR) Position Rest.
    3.85342e+05   -5.67173e+03   -1.17926e+06   -1.72551e+05    4.23618e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -9.31678e+05    2.39317e+05   -6.92360e+05    3.43853e+02    1.93620e+04

I put in my sistem a pressure of 1.013 bar, but I see a pressure of 
1.93e+04. The mdrun goes in segmentation fault...
I tried to run a NVT too, but nothing.
How can I follow?
Thanks in advance,

Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
Tel 051/6446992
FAX 051/2093690 

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