[gmx-users] AFM Pulling Simulations

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 26 20:56:10 CEST 2010


It would also be a good idea for you to ensure that your supervisor  
knows how difficult it is to learn and correctly apply these methods.  
If they think that a person can learn linux and gromacs and the  
gromacs pull code in a short period of time, then the stage is set for  
frustration and ultimate disaster.

Lots of people think that these things are plug and play -- of course,  
they are not.

If you don't have a mentor nearby who can help you, then figuring this  
all out and getting some meaningful data could easily take you a year.  
I don't mean to scare you off, but it is true that while no professor  
asks a new student to get protein crystals within a few months, that  
request is often made for simulation results from experimental  

Perhaps the gromacs community should be working toward getting  
testimonials to the significant amount of time that it can take to  
learn to run simulations properly on the gromacs site that new users  
could direct their supervisors to in the case that those supervisors  
are not acquainted with molecular simulation.


> 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

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