[gmx-users] Problem with accelerations
m.kamps at student.rug.nl
Wed May 24 11:28:59 CEST 2017
I'm not really sure what you mean by technique. I assume NEMD stands
for Non-equilibrium MD? That is the case in my simulation..
About my simulation: I am trying to simulate a fluid flow between
surfaces. Two atomistic surfaces of gold atoms have been created at
Z=0 and Z=z, where z is the top of the box. These surfaces are fixed.
In between is a fluid that should be accelerated in order to create a
flow. This is done by applying a constant acceleration in the X
direction via the commands; 'acc-grps = FLUID' and 'accelerate = 0.05
0 0'. Is this equal to the bug you referenced to?
Suppose the command is broken, does this mean that the simulation is
worthless since there are computational errors, or is the applied
velocity buggy but the results still useful? Suppose I can find the
right accelerations, can I still use the results?
Another question, how can I properly 'reply' to an answer working from
the digest mailing list? If I reply normally (via my mail client) and
delete the other messages, my message will not be displayed as a reply
in online mailing-list viewers such as Narkive etc. Am I replying
Mark Abraham wrote:
> 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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