Stefan Hoorman wrote:
Well, I tried again, this time simulating 1ns each window. I thought
about simulating more, but thought of making a test before making longer
simulations for nothing. And again, my histogram looks like a
chromatographic peak, but the range this time is different. The rest of
You should have overlapping roughly Gaussian distributions. I can't tell if
that's what you have, or if you have independent peaks. If the latter is the
case, then your windows do not overlap sufficiently to run WHAM.
the histogram is a straight line parallel to the x axis set in zero. I
Parallel lines indicate discontinuities in the WHAM analysis. I really think
you need to post an image of this online so we can see. Without seeing what
you're dealing with, it's very hard to be helpful.
didn't understand what you meant by "getting what you think you are
setting up". I have checked the distance between my groups, both with
g_dist and by visual aid. The separate all right, there is no doubt
about that. Each window is what it should be, a window for the 1.5nm
distance starts at 1.5, decreases a little bit in the first picoseconds
and then stabilizes at 1.47 or 1.45. When I start g_wham analysis, the
verbose states that my initial distance is 0.99nm and then it says that
"Determined boundaries to 1.046511 and 2.140948". I tried this time
Right, because your windows appear to range between these two values, so the
closest window is restraining your structures at roughly 1 nm, and the furthest
window is restraining the strucutres at 2.14 nm COM separation. Is this what
you expect? I thought before you were dealing with distances out to 2.5 nm.
simulating longer periods, and got the same result as before. The
profile graphic stars as a descending curve from 0 to -5 kCal, then it
starts rising in a "up the hill" way until it reaches +45kCal. I really
don't know what I am doing wrong this time.
Can you re-post the .mdp options you're using for pulling? Also, images of both
your histogram and profile would be extremely helpful. I'm having a hard time
picturing what you're describing with respect to the histograms.
-Justin
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
