[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force

[gozde ergin]

Maybe someone has an idea how to extract the instantaneous forces from the
trajectory.
I would normally use g_traj command to extract the forces however I am not
sure if this force means instantaneous force.


On Wed, Nov 25, 2015 at 2:02 PM, gozde ergin <gozdeeergin at gmail.com> wrote:

> Dear gromacs users,
>
> I would like ask a question about the force of umbrella sampling.
> I did umbrella sampling by pulling a water molecule from gas phase to
> organic coated bulk water.
> I estimated the free energy profile on this reaction coordinate.
> In order to calculate the random force-force auto-correlation I need to
> extract the random force on pulled molecule. The force along a reaction
> coordinate consists of three terms, (i) the mean force as the derivative of
> the free energy surface, (ii) friction, and (iii) random force.
> I used gromacs tool g_traj to extract the force on pulled molecule however
> I do not know how to get the random (iii) force out of it.
> I would greatly appreciate it if you kindly give me an advise about a way
> to extract random forces from the overall forces?
>
> Best regards
>
>
>