Natalie Stephenson wrote:
Hi,
I was wondering if you would be able to clear up a slightly confusing
aspect of the simulations I've been running.
I am currently performing a pull simulation and when viewing the outputs
of all the simulations I have run I see the extension of the protein
stop when it reaches the same sub-domain each time (at around a 10 nm
extension). The mdp file I use as the input file states that the pull
distance should be much larger than this.
Also when viewing the -px -pf outputs this agrees. When the simulation
reaches a 10 nm extension it stops and only increases around 0.2 nm over
the remaining simulation time (~3000 ps). When force extension is
plotted there is still an increase in force which results in a spike at
the 10 nm extension point, increasing the force from around 0.7 nN to
around 30 nN.
Is there any reason this could be an artefact or is it just the fact
that this domain is very firmly in contact with it's adjacent domain?
Is your box of sufficient size? Your pull distance must always be less than
half the box vector in the pulling dimension (unless using the
direction_periodic geometry, which may or may not be available in your Gromacs
version, but you haven't said which you're using). What type of unit cell are
you using? Could the protein be running into its own periodic image?
-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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