[gmx-users] Problem with accelerations

Mark Abraham mark.j.abraham at gmail.com
Tue May 23 14:35:32 CEST 2017


Which technique are you using for this?
https://redmine.gromacs.org/issues/1354 speculates that this code is just
broken, has been so for years, and should be removed given that nobody
wishes to do the work to fix it ( :-( )


On Tue, May 23, 2017 at 11:13 AM Kamps, M. <m.kamps at student.rug.nl> wrote:

> Dear GMX users,
> I have some strange behaviour which I cannot explain.
> I want to accelerate atoms through my box at a certain velocity. Since
> I can only adjust the acceleration, I have to trial-and-error my way
> to the right accelerations.
> To do this, I create a smaller 'testing' simulation, which is
> continued from an extensive equilibrium. I apply an acceleration of
> 0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with
> an gmx select input) says that the velocity is stable at around 0.04
> nm/ps. throughout the simulation the velocity slightly increases due
> to the atoms rearranging etc.
> Now I want to simulate the same behaviour, but for a longer amount of
> time. I therefore take the exact same MDP file, and change nothing
> except the time-related parameters. I change the number of total steps
> and the timestep, but leave the acceleration intact. After analysing
> the data I get a MUCH higher velocity! I can understand this due to
> rearranging of the atoms on the longer term, but after the same 200ps
> the velocity is also way higher.
> So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in
> this longer run, the velocity is 0.2 nm/ps after the same 200ps. How
> is this possible? The exact same acceleration is applied.
> Am I missing something?
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