Gavin Melaugh wrote:
Hi All
I am using COM pulling to pull two molecules together in order to
calculate the potential of mean force and the pulling is fine. I am
using pull = umbrella for the pulling as I am following
the tutorial on the website. If I use pull = constraint does this still
pull the molecules together, and if so do you still then need to
perform umbrella sampling on the configurations generated? I am a little
confused as I don't understand how the molecules pull together if they
are constrained.
For plain SMD, you can use any of the pull methods. In the tutorial I wrote, I
explain why I used "pull = umbrella" during SMD. Umbrella sampling is a
separate procedure, which can be done after SMD. If you want a free energy
along the reaction coordinate, there are several methods for doing this, among
which is umbrella sampling.
-Justin
Many Thanks
Gavin
Some additions to Justins comment:
If you want to perform the umbrella sampling (or calculating the pmf
form integrating the constraint forces) it doesn't really matter how you
obtain the structures for the different windows (but you will need them).
If you only want to perform the calculating of the pmf,
"pull=constraint" it's a little easier to get these structures. You can
perform your pulling so that each frame of the trajectory correspondents
to one structure and then extract them from the .trr / .xtc. Also the
pulling velocity doesn't really matter. If you pull with 1nm/ns and save
the coordinates every ns, then the distance of your molecules will
increase/decrease with 1nm between the different frames.
If you use the same setup with "pull=umbrella" the change of the
distance won't be 1nm but will depend on "pull_k1" the spring constant
with which you're pulling. So you must "search" the structures with the
right distances (for that is Justin's Perl script).
The nice thing with "pull=umbrella" is that you can see qualitativly
what happens during the pulling. If there is somewhere a barrier in the
pmf you will see it (more or less) that the distance between the two
molecules will change slower then if the is no barrier. With lower
velocity and spring constant (pull_k1) you will see that better.
But with "pull=constraint" you won't see that. Think the best way to
understand the difference between "pull=umbrella" and "=constriant" is
that the later is the first in the limit of an infinte "pull_k1".
Hope that helps. Good thing could be, take a small test system and play
around with the parameters and look what happens.
Greetings
Thomas
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