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
Thank you
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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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