[gmx-users] AFM Pulling Simulations

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 26 19:43:32 CEST 2010

Natalie Stephenson wrote:
> Hi,
> I'm a complete novice when it comes to using any kind of command prompt 
> based programmes and hadn't even heard of Linux until my supervisor 
> wanted me to use gromacs ... so needless to say I'm running into a few 
> problems!!
> I've managed to perform all the generic energy minimisations etc on my 
> protein (basically I can do everything that has been spoon fed to me on 
> the tutorial), but now I want to begin simulating AFM pulling 
> experiments.  I've printed (and bound!) the entire manual but I'm still 
> coming up against problems with understanding how I go about running the 
> AFM simulations.
> Does anyone have a basic syntax they have used to perform a similar 
> simulation so I can work from there and figure out what I need to put 
> where?
> Also, do I need to create any specific input files for these simulations?
> Thanks so much for your help with this...
> A rather inept gromacs user (Natalie!)
> xxx

There is a steered MD component to the umbrella sampling tutorial:


Though it is an excellent reference, the manual will not teach you everything 
you need to know.  The mailing list archive (although currently glitching) and 
Google are your friends, as well.  There are hundreds of threads in the archive 
about pull code success and failure, at least some of which should be informative :)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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