[gmx-users] monitoring position restraint energy

Erik Lindahl erik at theophys.kth.se
Thu Nov 15 23:36:07 CET 2001

David van der Spoel wrote:

> On Thu, 15 Nov 2001, David L. Bostick wrote:
> >I have thought about simply printing out the coordinates of Chloride and
> >calculating the restraint energy myself, but it would be nice if I could
> >just get this directly.  The manual says g_energy will give distance
> >restraint data, but nothing about position restraint data.
> You can do that with g_traj, and then a simple perl script or so will
> compute the distance for you. Isn't there some PMF functionality in the
> pulling stuff? Check the manual as I've never used it...

Yes, there is, but it was quite a while ago that I used it :-)

Check the umbrella sampling options for pulling; if you provide mdrun
with an empty input pull parameter file it will write a nice template output

file with all the available parameters. You do have to provide a reference
group, but that can be the rest of the system. Actually, I think that would
give an identical effect to position restraints since you normally reset the

center-of-mass motion each step, and if you are applying an external
position-restraining force on one atom only the system will get a small
net acceleration in that direction, and cancelling that motion probably
corresponds to applying a reaction force on the reference group.



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