[gmx-users] Pull code

David L. Bostick dbostick at physics.unc.edu
Wed Jan 22 16:35:56 CET 2003

Pertaining to the starting structures calculations ...

> > 3) Using "starting structures", it seems that the translation_rate
> > parameter is not in nm/step, because the induced translation
> > unreasonably faster.

I find it useful to constrain the groups that I am moving in the starting
structures calculations.  For example, if I am moving an ion in the
z-direction wrt a protein, I will use

freezegrps              = CL_pulled_ion
freezedim               = N N Y

Since the pulled group is subject to normal dynamics at every step, this
means that it can feel forces that cause movement in z other than the
update in the z direction produced by the starting structures code.
Constraining motion in z will keep the ion from flying off somewhere due
to unusual forces caused by placing the pulled group in a position it
would not ordinarily find itself.  This way, the system relaxes around the
pulled group and not vice versa.

Likewise, if you are pulling in an arbitrary direction, you can constrain
all dimensions.  This seems to work for me anyway...


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