[gmx-users] AFM Pulling Simulations

[Natalie Stephenson]

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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:
>
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>
> 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
>
> -- 
> ========================================
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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