Susana Tomasio wrote:
Hi all,
I'm running umbrella sampling of an ion through a lipid bilayer with
gromacs 4.5.1.
I used g_wham to create the histograms of the configurations within the
umbrella sampling windows (1 Angstrom interval).
I did not get a sufficient overlap between the windows, so I was
wodering which is the better way of increasing the sampling: to
include additional windows in the regions where there is no overlap or
to increase the force constant ?
If you increase the force constant, you will make the distributions narrower,
and thus I would expect the overlap would be worse. Insufficient simulation
length could be an issue, too, but you haven't said how long your simulations are.
If I increase the force constant can I continue the simulation with the
new constant or do I have to start again?
You'd have to start over again, I'd think, otherwise if you pass one .tpr file
to g_wham per window, it will contain incorrect information that will mess up
the calculations.
I used a force contant of 3000 kJ mol^-1 nm^-2.
That seems somewhat high, but there are no hard and fast rules about these
things, I don't think. You probably want either (1) a lower force constant or
(2) more windows along your reaction coordinate. Option (2) seems to be more
efficient, since you don't have to re-do your simulations, you can just run some
more.
-Justin
Thank you in advance,
Susana
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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/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
