[gmx-users] AFM Pulling Simulations
Natalie.Stephenson at postgrad.manchester.ac.uk
Thu Aug 26 20:05:36 CEST 2010
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> Natalie Stephenson wrote:
>> 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!)
> 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 :)
Thanks loads!! I'll give it a try! Natalie xxx
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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