[gmx-users] problems with rerun
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 25 03:50:42 CEST 2009
rsf wrote:
> 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.
I should add to what I said earlier - the neighbour searching only
affects the nonbonded interactions, and I was seeing small differences
in the bonded interaction energies. This suggests that you are not
comparing like with like. Thus you might be imposing a second round of
constraints, or taking structures from a limited precision .gro file, or
such like.
>
>> 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.
Read about these options in section 7.3 of the manual, then experiment
with varying one or two of them in a manner that seems sensible. You'll
learn much better this way than me prescribing something that may or may
not suit your actual needs, since I don't know what they are!
http://oldwiki.gromacs.org/index.php/Doing_Restarts may have a bit of
help, but it is not intended for GROMACS 4.
Mark
>> 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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