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.
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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