Stefan Hoorman wrote:
Stefan Hoorman wrote:
I am starting again my calculations for the real system and this am
going to use as starting positions distances in intervals of
0.1nm. Some
of them aren't really 0.1nm apart since the distance between the
twogroups in my first trajectory does not always increase in a steady
way, but the average distance between them is close enough to
0.1nm. I
looked back in the mailing list and found something about applying
restraints to these simulation windows. I imagine these
restraints refer
to the umbrella potential still on and not actual restraining as in
adding -DPOSRES, right?
Without a link to the post you're reading, I can't comment on that.
It probably
refers to the umbrella biasing (restraining) force, but without
context, that's
just a guess.
One other thing I've noticed is that the distance between my groups
decrease in several of my windows, as one would expect since the two
structures still interact with each other, and in some cases they get
back to the original distance prior to the separation. Is this normal
for the WHAM analysis?
I don't understand what you mean. There should be some fluctuation
about a mean
position in each window. The umbrella potential maintains this
distance, on
average, if you're doing things right.
Justin
Ok, here is what I meant. I use each of the starting position extracted
from my original pulling trajectory (i mean the trajectory with
pull_rate = 0.01) to simulate each window. Each of these windows
still have the umbrella force constant (pull_k1 = 35) but now have
pull_rate = 0. My system, though, does not fluctuate about a mean
position in each window. My system returns to the initial dimer or tries
to if the distance is too big and the simulation time not long enough.
So, whem I analyse the distance between the two groups with g_dist in
each of the sampling windows, I get a series of decreasing values that
will eventually return to the 0.9 nm.
For these simulations, I keep the same parameters as in the original
pull trajectory. The vectors are still the same, the force constant is
still the same. I only change the pull_rate from 0.01 to 0 and
pull_geometry from direction to distance (because g_wham asks tells me
pull_geometry = direction is not supported).
So maybe I am doing something wrong.
If the starting structures are not staying in the desired windows, it seems to
me that your force constant is not large enough to maintain these positions.
Try something larger, like 500 or 1000 like I suggested before and see if you
get a better result.
-Justin
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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