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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