On 9/21/12 8:29 AM, Bastien Loubet wrote:
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane using the coarse grained
Martini force fields. From these simulations we obtained a trr trajectory
file which contains both the position and the velocity of each martini
particle every 20 ps. From this trajectory we rerun the simulation using the
-rerun option of the mdrun program but with a different topology for which
we have set all the bonded and non bonded interaction to zero. Specifically
we have set all the force constant to zero in the martini_v2.P.itp and the
martini_v2.0_lipids.itp file, the aim is to calculate the virial due to the
electrostatic forces alone.
The problem is the following: from the edr file we get from the rerun we
extract the mean value of the energies using g_energy. For the edr file
obtained during the simulation (and not the rerun) we obtained for the
temperature and the kinetic energy, using also a 20ps time interval:
Energy Average Err.Est. RMSD Tot-Drift
---
Temperature 324.998 0.0049 0.413669 -0.00743801 (K)
Kinetic En. 1.9525e+06 292485.21 -44.6815
(kJ/mol)
This is to be expected because we have a Nose-Hover temperature coupling of
325 K. The kinetic energy is also equals to the number of degree of freedom
times half the Boltzmann constant times the temperature.
However for the rerun, with no bonded and non-bonded interactions, we get:
Energy Average Err.Est. RMSD Tot-Drift
---
Temperature 327.35 0.0053 0.415978 -0.00514402 (K)
Kinetic En. 1.96663e+06 322499.08 -30.8973
(kJ/mol)
The kinetic energy is again equals to the number of degree of freedom times
half the Boltzmann constant times the temperature, however the temperature
is 2 K off ! This is surprising as only the velocities and the masses of the
particle should enter the kinetic energy. The velocities are taken from the
trr trajectory file and we have checked using the Linux diff utility that
our topology have the same masses than the original one.
Another cause can be that we are doing the rerun on a local machine while
the original simulation was run on a cluster, however we believe that this
kind of numerical error cannot be responsible for a 2 degree Kelvin mistake.
Furthermore we have rerun the simulation using the original topology and we
obtained:
Energy Average Err.Est. RMSD Tot-Drift
---
Temperature 324.998 0.005 0.411827 -0.00761929 (K)
Kinetic En. 1.9525e+06 302474.15 -45.7788
(kJ/mol)
The slightly different value are certainly due to the previously mentioned
fact that the reruns were not run on the same machine as the simulation and
numerical rounding errors. This point out that it is really the topology
that changes the value of the temperature. However we really have no masses
differences between the two topologies and the velocities are draw from the
same trr trajectory file.
Any thought on this problem would be welcome.
Another thing to consider is the fact that an .edr file is accurate over all
simulation steps, while reruns only do calculations present in the frames
supplied. If you are using frames every 20 ps, that may only represent less
than 1% of the total data collected in the simulation, depending on the value of dt.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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