[gmx-users] AFM pulling options

Justin MacCallum jlmaccal at ucalgary.ca
Thu Aug 1 00:09:03 CEST 2002

Hi Ernesto and Alicia,

what version of Gromacs are you using?  I have been working on the AFM 
and umbrella sampling code for a while now.  I think I've finally merged 
all of our changes into the CVS tree now, but the changes are not in a 
currently released version of Gromacs, so you'll have to download and 
install the CVS version using the instructions on the website.  The new 
version of the pull code will (optionally) write out the .pdo file as a 
compressed version (with gzip), so you may need to view it with "zcat 
filename.pdo".  It also now prints a header at the top of the file with 
the name of the pulled and reference groups and spring constants, etc. 
 The rest of the data is now in the format "position_of_pulled_group     
  spring_position".  From this you can easily calculate the force vs 

I have run some tests with the new version of the pull code, but they 
haven't been exhaustive by any means.  If you find any problems please 
let me know and I'll fix them up as soon as I can.


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