[gmx-users] problems with rerun
rsf
romelia at caltech.edu
Mon Aug 24 23:46:43 CEST 2009
Hi I have a molecule described by two sets of parameters (in atom
connectivity and coupe values of bond interactions) and I need to get the
energy difference between those two descriptions. I have been having
problems with the rerun capability (I am using the latest version of
gromacs)
I did the following tests, I will include only the energy components for
the first step of the trajectory for each state after a steepest descent
run for each state.
Running an md calculation with state 1:
result during md simulation
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.81497e+02 9.71604e+02 1.09286e+03 2.84503e+02 1.34015e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.69155e+04 2.28027e+04 -2.23828e+03 -2.79565e+05 -3.31702e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.11970e+04 0.00000e+00 -2.53835e+05 2.27203e+01 -2.53812e+05
Temperature Pressure (bar)
1.64402e-01 -1.23399e+04
result extracting the configuration from .trr file and runing a single
step md
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.81948e+02 9.72103e+02 1.09285e+03 2.84608e+02 1.33985e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.69153e+04 2.28365e+04 -2.23835e+03 -2.79562e+05 -3.31715e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.11970e+04 0.00000e+00 -2.53797e+05 2.39171e+01 -2.53773e+05
Temperature Pressure (bar)
1.73062e-01 -1.22928e+04
using rerun
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.81497e+02 9.71604e+02 1.09286e+03 2.84503e+02 1.34015e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.69155e+04 2.28027e+04 -2.23828e+03 -2.79565e+05 -3.31702e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.11970e+04 0.00000e+00 -2.53835e+05 2.27203e+01 -2.53812e+05
Temperature Pressure (bar)
1.64402e-01 -1.23399e+04
For state 2:
result during md run
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
1.64555e+02 9.37861e+02 1.09286e+03 2.82162e+02 1.44514e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.65633e+04 2.27962e+04 -2.23852e+03 -2.79767e+05 -3.27838e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.12594e+04 0.00000e+00 -2.54562e+05 1.69486e+01 -2.54545e+05
Temperature Pressure (bar)
1.22639e-01 -1.22600e+04
result extracting the configuration from .trr file and runing a single
step md
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
1.64743e+02 9.38358e+02 1.09285e+03 2.82134e+02 1.44485e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.65631e+04 2.27975e+04 -2.23859e+03 -2.79766e+05 -3.27859e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.12594e+04 0.00000e+00 -2.54560e+05 1.70085e+01 -2.54543e+05
Temperature Pressure (bar)
1.23072e-01 -1.22427e+04
using rerun
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
1.64555e+02 9.37861e+02 1.09286e+03 2.82162e+02 1.44514e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.65633e+04 2.27962e+04 -2.23852e+03 -2.79767e+05 -3.27838e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.12594e+04 0.00000e+00 -2.54562e+05 1.69486e+01 -2.54545e+05
Temperature Pressure (bar)
1.22639e-01 -1.22600e+04
Now, taking the trajectory from state one and running with state two I get:
result extracting the configuration from .trr file and runing a single
step md
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
1.67952e+02 9.49784e+02 1.09257e+03 2.99138e+02 1.44148e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.65629e+04 2.27997e+04 -2.23860e+03 -2.79766e+05 -3.27896e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.12594e+04 0.00000e+00 -2.54527e+05 1.80405e+01 -2.54509e+05
Temperature Pressure (bar)
1.30540e-01 -1.22544e+04
using rerun
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
1.65324e+02 9.59476e+02 1.09288e+03 2.86607e+02 1.44651e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.65630e+04 2.28061e+04 -2.23879e+03 -2.79719e+05 -3.28984e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.12594e+04 0.00000e+00 -2.54489e+05 2.60448e+03 -2.51885e+05
Temperature Pressure (bar)
1.88458e+01 -1.28402e+04
And finally, taking the trajectory from state two and running with state
one I get:
result extracting the configuration from .trr file and runing a single
step md
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.81985e+02 9.72096e+02 1.09285e+03 2.84475e+02 1.33994e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.69153e+04 2.28359e+04 -2.23835e+03 -2.79562e+05 -3.31715e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.11970e+04 0.00000e+00 -2.53798e+05 2.38608e+01 -2.53774e+05
Temperature Pressure (bar)
1.72654e-01 -1.22933e+04
using rerun
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.81723e+02 9.95438e+02 1.09288e+03 2.81996e+02 1.33794e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
1.69154e+04 1.01156e+05 -2.23847e+03 -2.79572e+05 -3.32791e+03
RF excl. Position Rest. Potential Kinetic En. Total Energy
-1.11970e+04 0.00000e+00 -1.75478e+05 1.99111e+07 1.97356e+07
Temperature Pressure (bar)
1.44075e+05 1.30412e+06
The rerun using the same parameters as the original md seems to give the
right answer while recalculating the energy extracting the configuration
from the trr file differs a little but it still gives values similar as
those obtained from the rerun and the original md. In the case of the
resuts obtained by changing the parameters the values obtained by doing a
rerun or extracting the configuration from the trr file differ
significantly from eachother. Could someone suggest what I could be doing
wrong. Thanks!!!
--
****************************************
Romelia Salomon
Chemistry Department
Caltech
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