[gmx-users] Pull code

Michel Cuendet michel.cuendet at epfl.ch
Tue Jan 21 19:01:36 CET 2003

  I am trying to make free energy measurements for the exchange of a 
water molecule around a sodium ion via the Jarzynski method. The 
principle is simple, steer a water towards the ion, and integrate the 
forces. This system is maybe unusual for gromacs, but according to the 
weird trajectories I get, it is doubtfull that the code work correctly 
for any system...

  Here is a series of questions :

1) When all groups are specified, why does mdrun ask for a group? The 
group specified here doesen't seem to  influence the results.

2) Using AFM, when a group crosses the box boundary, it is replaced b 
its image on the other side of the box. But the steering potential stays 
centered where it was, which results in an enormous force on the pulled 
group, and fast crossing of the box.

3) To prevent this, I decided to remove the center of mass motion of the 
ion, and steer the water towards it. But then it apprears that the 
effective steering velocity is not correct, as if it was not affected by 
the CMM removal.

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

4) Using "starting structures", is the constraint also characterized by 
the AFM forceconstant parameter?

5) Using "starting structures", the steered group doesn't really go to 
the reference group, but it passes about 3,5 A from it and continues 
further. In which direction?? - "The truth is up there" (Mulder)

  Help me out, please, I'm getting nuts with this.


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