Gavin Melaugh wrote:
Yeah
I set pull_init =0, and pull_start = yes, and it still gave a "distance
at start" as 0.78nm. It must be doing something funny because with
pull_vec, because when I use pull_geometry = distance and pull_dim
= Y Y Y, the distance 0.815nm is returned as the "distance at start",
which is the actual distance between the two groups.
I have no idea why this is happening. If you'd like me to troubleshoot further
and see if I can get to the bottom of this, please send me (off-list is OK):
1. Coordinate file
2. Topology file(s)
3. The .mdp file that is giving the weird result
-Justin
Cheers
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
Sorry maybe I was unclear before with my first point; the specified
distance in the mdp file is 0.78nm, which grompp returns back as the ref
distance. The "distance at the start" that grompp returns is also
0.78nm, even though the actual distance is 0.815nm. That's why I was
asking what this distance actually means, as it is not the absolute
distance between the reference groups.
As I said before, you're telling grompp to make that the reference
distance. You say "the specified distance in the mdp file is 0.78 nm,"
therefore grompp is doing what it's told. If that's not the desired
distance, then don't set it as such. Have you tried the combination I
suggested in the last message? Does it give an initial distance of
0.815 nm?
Also as regards to your second point; what if in the initial
configurations the two reference groups do not lie along the stated
vector?
Hard to say, but probably you'll get some very high forces at the
outset of the simulation as the simulation as the umbrella potential
tries to force the pulled group to conform to the restraint
specifications. Whether or not that negatively impacts the ultimate
result of the simulation is also an important consideration. If
you're pulling along a given vector, you should start with your
reference coordinates as close to the desired location as possible.
-Justin
Cheers
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Justin
I did a short test on a particular window with the specified vector
with
pull_init =0.78nm. I then grompp(ed) the final configuration and it
gave
me a distance of 0.78 as the initial ditsance, fair enough. However
when
I viewed the final line from g_dist the absolute distance or
modulus was
0.815 nm, which agreed with the distance I calculated using a
molecular
configuration editor. My question is therefore this, when using
pull_geometry =direction with a specified vector, How should one
interpret the initial distance provided by grompp? and how does
Gromacs
deal with the fact that the vector between the two point changes
during
the run ?
You're telling grompp that the initial distance is 0.78 nm, so it's
spitting that back out. If that's not the true distance, then specify
the correct quantity :) The distance should be correctly detected
with:
pull_start = yes
pull_init = 0
As for the second question, the vector doesn't change over the
simulation, but the position of pull_group1 along that vector will.
That's what the umbrella potential is doing - it allows for harmonic
oscillation along any of the dimensions specified by pull_vec/pull_dim
(depending on the settings).
-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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