On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote:
Hi Xavier
Many thanks. Two more quick questions (both refering to barrier
region):
Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap?
No! The force constant used does not affect the PMF or the barrier.
Neither
does the number of windows used. The only thing that can affect your
PMF is a change in the sampling you put in ...
Obviously there is a
compromise between the size of the constant and the number of windows.
True! And the objective being to get equilibrated distribution with
reasonable
overlaps.
If I increase the force constant and number of windows to obtain a
high
density of sampling, does this give a more accurate curve?
No! The only thing you need is to sample everything. Actually putting a
strong force constant might have the side effect to trap your system and
then you do not sample the "free" degrees of freedom! With weak force
constant you may have to wait very long to obtain an equilibrated
distribution.
XAvier.
Gavin
XAvier Periole wrote:
On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:
Hi Xavier
Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased
force
constant (note I have only increased the force constant of the
windows
in the barrier region).
Force constant =1000, Force constant in barrier region = 5000
The barrier increases due to better sampling in this region
(expected),
but the rest of the curve in 2) is shifted upward compared to
curve 1).
Why is this so when the only difference is the increased number of
windows and force constant in one region?
the relative position of the regions on the left and right of your
"barrier"
region is completely depending on the barrier region!
you may have overestimated the difference between bound/unbound
states
because the energy barrier region was not sampled.
Note also that cure one is simply wrong so comparing to it is
dangerous.
You have to be careful that you might still not have a converged
sampling:
you might have overlap of your histograms on the reaction
coordinate but
other degrees of freedom are not fully sampled ... that might
result in a
funny and wrong profile. You might want to look at your simulations
for
funny things ...
Gavin
XAvier Periole wrote:
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
Dear all
I have generated a PMF curve for introducing a guest molecule
into a
host molecule using the umbrella sampling method. The curve seems
fine,
but there are no overlaps between histograms in the barrier
region. To
circumvent this I have added more windows in this region and to
ensure
sampling have increased the force constant only in this region.
The
windows in this problematic region are now not equally spaced.
Does
this
matter for g_WHAM?
Nope it does not matter.
Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?
Many thanks
Gavin
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
