Gavin Melaugh wrote:
O.K thanks anyway
I saw the plots you posted during a conversation with Chris, but I'll ask the
obvious anyway: have you watched the trajectories for any of the problematic
windows? It didn't seem like you had two metastable states, but maybe having a
look at the movie would shed some light on what's going on. I know that's the
first thing I'd do.
-Justin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Thanks Justin
Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.
Sorry, no clue.
-Justin
Cheers
Gavin
Justin A. Lemkul wrote:
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.
Pull group natoms pbc atom distance at start reference at t=0
0 72 36
1 72 360 4.290 4.290
why is this so?
grompp always assigns the numerical middle atom of a group as the PBC
...unless over-ridden by providing a different value for pbc_pullatom1.
-Justin
reference point. In the case of pbc=no, it shouldn't matter.
http://manual.gromacs.org/current/online/mdp_opt.html#pull
-Justin
Cheers
Gavin
--
========================================
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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