Gavin Melaugh wrote:
I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file
That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference group, then
displacement (dX,dY,dZ) of the pull group relative to the reference. Not all
terms may be present, depending on the axis along which you're pulling, i.e. if
you only pull along Z, there will be two terms in pullx.xvg - Z and dZ.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Justin
I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 250000 steps for every 50000000 step
simulation (100 ns). Ill look at them again in more detail and post
back.
Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur. Mapping
that information back onto the trajectory could help focus your
attention.
-Justin
Gavin
Justin A. Lemkul wrote:
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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