On 26/08/10 19:56, chris.ne...@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*.
m.
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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