Dear GROMACS developers and users,
I have a question regarding GROMACS force output. I need the
total force on each atom at every timestep in a constant temperature MD
trajectory. I am using the Nose-Hoover thermostat for constant temperature
simulations. I know that by using the 'nstfout' keyword in the .mdp file I can
tell GROMACS to output forces in the trajectory (.trr) file. Now my question is
what exactly is written in the output file as "force" when I use the above
mentioned option.
I understand that at first this question may seem a little
strange and unnecessary, since everybody knows what a force is, but in the
context of Nose-Hoover dynamics there is a slight chance of potential confusion
as discussed below. The force information is very crucial for our subsequent
analysis, that is why we wanted to make sure that we know exactly what is being
printed when one uses the 'nstfout' keyword.
Total force on a particle can be interpreted as either the
negative gradient of the total potential energy with respect to the position of
the atom in question OR the instantaneous rate of change of momentum of the
atom. Now for normal Hamiltonian dynamics both of these definitions will give
the same number but for the Nose-Hoover dynamics they will be different.
Because in the Nose-Hoover equations the rate of change of momentum of an atom
is a sum of two terms, first term is the negative gradient of total potential
and the second term is momentum of the particle multiplied by a thermostat
parameter. So, in Nose-Hoover equation instantaneous rate of change of momentum
is NOT equal to the negative gradient of the potential with respect to the atom
position.
In the light of above discussion can anyone please tell me
when GROMACS prints forces in the trajectory file during a Nose-Hoover
dynamics, which quantity does it print? Is it the negative gradient of the
total potential with respect to the atom position OR the total instantaneous
rate of change of momentum which includes an extra term?
Thanks a lot,
Avisek
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