[gmx-users] Force output
avisek at stanford.edu
Tue Apr 20 03:10:33 CEST 2010
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,
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