Quoting "Justin A. Lemkul" <jalem...@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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