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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