I think this one can help you:
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000306
You can download a code that gives you the forces from the following website:
http://projects.eml.org/mbm/website/fda_gromacs.htm
Ilona
Quoting Avisek Das <avi...@stanford.edu>:
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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
