[gmx-users] problems with rerun
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 25 00:17:39 CEST 2009
rsf wrote:
> 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.
Proper procedure would be to obtain a trajectory file with the
structures of interest, and then to construct a .tpr file suitable for
each model physics, and then to use -rerun on the same trajectory file
with each .tpr file.
> 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.
That's normal. -rerun does neighbour searching every step, so it will
differ slightly at all steps for which the original run did not do
neighbour searching.
You also need to choose sensible combinations of unconstrained_start,
gen_vel, extracting a trajectory frame for which velocities were
written, and not accidentally taking coordinates from a .gro file.
You're probably using a confused combination of all of the above for all
of your different tests.
Make sure you are using 4.0.5 as -rerun was broken in some earlier version.
Mark
>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!!!
>
>
>
>
>
>
>
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