The easiest solution would be using 'pull_geometry = distance' in all
three dimensions. Then you can be sure that both groups are pulled
together. Small remark: One group would be fixed for the pulling, and
the second group gets pulled towards the first group. So if you want to
have both groups really close, this setup would be the easiest solution.
If you really to pull both groups to a point in the middle between them,
i think you would need 'pull_geometry = position':
Use some part of the DNA as the reference group and put the origin of
the pulling (via 'pull_init') to the middle point. Then make two
pull-groups + 'pull_vec1' or 'pull_vec2', from each DNA part, which you
want to pull to the middle point.
In principle this setup should work, but you can run into problems if
the structure of the DNA changes and the middle point, to where you pull
both groups, moves somewhat around.
hard to explain...
I would stick to the first approach...
What pull-mode did you use? You could use 'pull = constraint', measure
the distance between both groups and then pull with a given pulling
velocity so long till both groups should meet. Since you use a
constraint instead of a restraining potential, the groups should be
definitly pulled together (or some other parameters in the .mdp file are
wrong).
Greetings
Thomas
Am 27.03.2013 20:16, schrieb gmx-users-requ...@gromacs.org:
Hello All,
My simulation system is composed of DNA and want to pull both of the primes
at the same time towards each other.
I have tried every possible set of parameters in pull code...and i am not
able to pull them together.
it's like ...
the DNA molecule is aligned along Y-axis and if want to pull both ends at
the same time that means pulling in -Y and +Y direction at the same time.
if anyone successfully implemented such ...simulations... Please provide me
with some idea about this problem.
Thank you
Raghav
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