[gmx-users] AFM Pulling Simulations

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Thu Aug 26 19:17:53 CEST 2010


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  

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!)

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