[gmx-users] Re: Pulling Code

Justin MacCallum jlmaccal at ucalgary.ca
Sun Nov 10 22:17:36 CET 2002

Hi everyone,

I apologize for the current bugs in the pull code. It should have been more
thoroughly tested before being released, but at this point I just don't have
the time. I am doing my best to try and clean up the existing problems, and
hope to have some more time to work on it soon.


> Hi Frauke,
> It's great to know that someone else is working with the pull code; we can
> our efforts! I sent to Justin, as he requested, the impute files of the
> I'm working on, as well as the file.ppa (output file). I hope that he had
> some time to deal with them! I never tried to pull two groups
> so I don't know about that problem. What I think is that it would be
better if
> we could chouse the pulling direction ( -z or +z ) for each pulling group,
> instead of considering a reference group and chouse a "from_reference"
> or "to_reference" parameter to define this directions. Maybe in your case
> which you are dealing with two groups separating one from each other, it
> be confusing which is the reference group for each of each of the pulling
> groups, if I understood it correctly.
> I'm adding to this mail part of what I sent to Justin in reference to the
> option. It might be of any help to you or anyone else working on this:
> "We are attaching the pull.pdo file of this simulation. From this file we
> obtain the pulled_group_position (first column) and the spring_position
> column) so we calculate the force as:
> spring_elongation = [pulled_group_position( t) - spring_position (t)] -
> pulled_group_position( t = 0),
> force = spring_elongation * k
> since the spring_position is always initially at the origin and the force
> should be zero at t = 0.
> Since we have developed our own program where so far can do afm
simulations in
> an effective medium, we try to compare our simulations with the Gromacs'
> the same approach. When we do so, we set the parameter 'nstcom' = 0 (in
> the .mdp file) but it was not accepted (only -1 is compatible in effective
> medium simulations). We did not encounter this problem in the hydrated
> This is important because removing the kinetic energy by controlling the
> of mass velocity, will affect the dynamic behavior of the system and it
> interfere in the determined force value.
> By the way, the improvements mentioned by Baaden are quite important and
> would be great if you could take them in consideration, though he got a
> different way to determine the force, which I would like to discuss with
him to
> see his point of view".
> Will keep in touch,
> Cheers,
> Alicia
> --__--__--

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