[gmx-users] AFM pulling rate

Berk Hess gmx3 at hotmail.com
Thu Aug 14 10:08:57 CEST 2008


The pull code in Gromacs 3 is pretty messy.
The rate is in nm/ps.
The force is (unfortunately) not written to the pdo file.
You have to redetermine it from the positions,
but beware that one of the two groups could jump over the periodic boundary.

In Gromacs 4 (and the current CVS) I have completely rewritten the pull code.
There are separate xvg output files with only the positions and only the forces.


> Date: Thu, 14 Aug 2008 08:30:35 +0200
> From: malbe at kth.se
> To: gmx-users at gromacs.org
> Subject: [gmx-users] AFM pulling rate
> Hi,
> The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps.
> I have read something in an earlier thread on this list that this might 
> be a typo, it should be nm/timestep. Does anyone know? I would be happy 
> if I could have that information.
> Moreover, I am a bit confused about the output in the .pdo-file.  In the 
> description of  .pdo-files on page 113 in the manual 3.3.-1 it is 
> written that the .pdo file will contain calculated forces from 
> AFM-pulling simulation. On the other hand, on page 118, the description 
> of the AFM output is that it only contains positions of reference group, 
> pulled group and spring. This is also the only information I can find in 
> my output. I wonder if there is a way to get the calculated force into 
> the pdo file or if it should be done manually (force=k*extension)?
> /Malin Bergenstråhle
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