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 :)
-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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