[gmx-users] Re: Pulling Code

zhang ray zhangray7823 at msn.com
Tue Nov 12 07:43:49 CET 2002

Hi, Justin & everyone,
   I want to do some simulation about the "pull" with gromacs, but the 
description of some files such as "pull.ppa" are not included in the online 
document, could you please give me a copy of these files or examples.

Thank you very much in advance!


>From: "Justin MacCallum" <jlmaccal at ucalgary.ca>
>Reply-To: gmx-users at gromacs.org
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] Re: Pulling Code
>Date: Sun, 10 Nov 2002 14:17:36 -0700
>Hi everyone,
>I apologize for the current bugs in the pull code. It should have been 
>thoroughly tested before being released, but at this point I just don't 
>the time. I am doing my best to try and clean up the existing problems, 
>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 
> > 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 
> > 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 
> > instead of considering a reference group and chouse a "from_reference"
> > or "to_reference" parameter to define this directions. Maybe in your 
> > which you are dealing with two groups separating one from each other, 
> > be confusing which is the reference group for each of each of the 
> > groups, if I understood it correctly.
> > I'm adding to this mail part of what I sent to Justin in reference to 
> > 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 
> > 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 
> > 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 
> > 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 
> > medium simulations). We did not encounter this problem in the hydrated
> > This is important because removing the kinetic energy by controlling 
> > 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 
> > 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 
>him to
> > see his point of view".
> >
> > Will keep in touch,
> > Cheers,
> > Alicia
> >
> >
> > --__--__--
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