[gmx-users] strange jumping in the frames

Fahimeh Baftizadeh Baghal fbaftizadeh at yahoo.com
Fri Sep 10 09:57:33 CEST 2010


I am running Metadynamics with gromacs, I saw a jump in the frame after 
the simulation was running for a while, I copy here part of the log file:
           Step           Time         Lambda
       20557500    41115.00000        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    3.54705e+03    2.44201e+03    1.44990e+03    1.94769e+04    2.63535e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.09459e+05   -5.86065e+04   -2.14796e+05    5.09371e+04   -1.63859e+05
  Conserved En.    Temperature Pressure (bar)  Cons. rmsd ()
   -1.66948e+05    3.47266e+02   -2.03134e+02    2.74833e-05

DD  step 20559999  vol min/aver 0.846  load imb.: force  0.4%

           Step           Time         Lambda
       20560000    41120.00000        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    3.36185e+03    2.48355e+03    1.45350e+03    1.94714e+04    2.67211e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.09297e+05   -5.86137e+04   -2.14420e+05    5.18801e+04   -1.62540e+05
  Conserved En.    Temperature Pressure (bar)  Cons. rmsd ()
   -1.67082e+05    3.53695e+02    7.73024e+01    2.66928e-05

DD  step 20562499  vol min/aver 0.825  load imb.: force  0.6%

           Step           Time         Lambda
       20562500    41125.00391        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    3.55493e+03    2.49077e+03    1.45219e+03    1.93942e+04    2.60391e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.08596e+05   -5.86454e+04   -2.14310e+05    5.14416e+04   -1.62868e+05
  Conserved En.    Temperature Pressure (bar)  Cons. rmsd ()
   -1.67250e+05    3.50706e+02   -3.50552e+02    2.93757e-05




as you can see the time jumped from 41120.00000       to 41125.00391 , 
while it has to be 41125.00000 and then it continue the rest of 
simulation like this,
Do you what is the problem ?!!

Fahimeh




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