[gmx-users] Constrained MD questions
ababakha at mccammon.ucsd.edu
Tue Aug 29 23:20:00 CEST 2006
Hello GMX Users,
I have some specific questions about the constrained MD run options, as
explained on page 116 (in the Special Topics section) of the GMX manual.
1. Regarding "constraint_direction = " What exactly is the meaning
of the 3 values inputted here? Does 1.0 0.0 0.0 mean the x-axis?
(If so, why is this not in the "Y N N" format?) Or are these values
supposed to be angles?
2. Also regarding the "constraint_direction", the manual states that if
left in it's default setting (0.0 0.0 0.0), the distance between groups
is constrained. What if you only have one group? Then is the distance
between that group and the reference group constrained?
3. Regarding the "constraint_distance" The manual states that if left
in default (= 0), then the distance is determined by the starting
coordinates. But what distance are we talking about here? The distance
between the center-of-mass of the group, and that of the
reference_group? For instance, if the center-of-mass of group_1 is 1 nm
from the COM of the reference_group in the starting coordinates, then
setting constraint_distance1 = 0 will constrain this distance to 1 nm.
Is that correct?
4. Is the "pulldim" line necessary, if you're not doing AFM?
Thanks for the help,
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