Gavin Melaugh wrote:
Hi Justin
Many thanks for the reply I know technically I am doing two different
things. However due to my starting conifgurations in both cases I would
expect similar results.
Could you confirm the following points
1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
distance between the COM of both groups in all directions considered ?
Yes.
2) In pull_geometry = direction, with a specified vector; I assume that
it is the distance between the two groups along this vector that is
considered?
Should be. Compare the output of g_dist with what grompp reports as the initial
distance.
3) Is the specified vector taken to be the vector connecting the two
points? Therefore are the desired distances in the mdp files essentially
the magnitudes of this vector at each window.
Per the documentation, grompp normalizes the vector, so no, not directly. But
if you have proper settings for pull_init/pull_start, then the reference
distance should be correctly calculated along the specified vector for each 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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