Gavin Melaugh wrote:
Hi Justin
I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)
If you generate velocities without doing equilibration, then your system may not
be at equilibrium and thus you are doing inaccurate sampling. Thus, if your
system gets kicked in the wrong direction, the umbrella potential may have to
fight to pull the desired group back to where it thinks it should be, might be
overcompensating, etc.
-Justin
Cheers
Gavin
Justin A. Lemkul wrote:
Have you watched the trajectory? That will show you what your pull
group is doing. Is this a periodicity effect? It should be fairly
obvious iff the sign of dX, etc flip-flops in the pullx.xvg file.
-Justin
Gavin Melaugh wrote:
Thanks Chris and Justin
I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.
Pull group natoms pbc atom distance at start reference at t=0
0 84 42
1 84 126
5.507 5.507
Cheers
Gavin
[email protected] wrote:
I missed that pull_start = yes, sorry. So Gavin, your run should have
stayed around the starting position. Make the histogram directly and
you should get a better idea.
Chris.
-- original message --
To clarify, the tutorial sets "pull_init1 = 0" because it is used in
conjunction
with "pull_start = yes," in order to take the starting COM distance as
the
reference. Check the grompp output to verify that you're getting what
you think
you should be. Otherwise, you'd have to set "pull_start = no" and
modify your
.mdp file to reflect the proper value of pull_init1 for every window.
-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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