[gmx-users] problems with rerun

[rsf]

Mark
Thanks for your reply, I do prepare a .tpr file for each run. I run the
original md run and then I run grompp using the files with my modified
topology I need and then run with the -rerun option as you said. I am
using gromacs 4.0.5 since I saw in the notes for the release it had been
fixed. I think the problem should be what you said about the neighbour
list, etc.

> 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.

What would be a sensible combination for these? Thanks so much for your
help, I think I have a better idea of what I'm doing wrong.




> 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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-- 
****************************************
Romelia Salomon
Miller Group
132 Noyes
Chemistry Department
Caltech