For umbrella sampling you need to steps:
1) get the configurations for the later umbrella sampling (step 5 in
Justins tutorial). How you perform the pulling sim. for that isn't
important, you only need the structures.
2) umbrella sampling (step 6 in tutorial). Here you use the
configurations from step 1. I think here you can only use
"pull=distance" (i think).
Greetings
Thomas
Thanks Thomas
That has made things a lot clearer, but just to be sure. If I pull the
molecules using pull = constraints, do I still have to run umbrella
sampling on the generated configurations in order to calculate the PMF?
Also if I use pull_geometry = direction for the pulling can I use it for
the umbrella sampling with the intention of then using g_wham for the
analysis?
Many Thanks
Gavin
Thomas Schlesier wrote:
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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