[gmx-users] AFM Pulling Simulations

ms devicerandom at gmail.com
Mon Aug 30 17:20:44 CEST 2010

On 26/08/10 19:56, chris.neale at utoronto.ca wrote:
> Natalie:
> 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 supervisors.
> 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.

I couldn't agree more. I have been thrown into learning GROMACS and 
designing a coarse grain model from scratch (my background is that of an 
experimentalist, doing AFM pulling experiments, by the way!), all 
practically by myself. I mean: I *wanted* to learn all of that, I just 
didn't expect I would have done it *alone*. So I read the Frenkel-Smit 
book, the GROMACS manual, and banged my head a lot (luckly I was already 
experienced with Linux and programming). No wonder one year after, I'm 
just beginning to see where I am going *sigh*.


> Chris.
>> 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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