Dear gmx users,
my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one
is pulled from the other. I followed Justin's tutorial on umbrella sampling.
Here are the results.
profile.xvg:
http://przemekbartha.pl/upload/profile.png
histo.xvg:
http://przemekbartha.pl/upload/histo.png
I would be grateful, if anyone could tell me why is the PMF so irregular,
unstable, unlike the courve in the tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/07_analysis.html
After a little bit of research on "gmx-users", my guess is either incorrent
sampling or/and some major mistake in parametrization.
I tried to resample the simulation so that the "umbrellas" don't overlap as
much as they do in my histo.xvg file but it changed the PMF totaly and did not
resolve the problem.
Or maybe, it is just the way it should be?
My pullcode is nearly the same as in the tutorial. I don't want to trash, but
if you require any additional information, please let me know.
The sampling is twice as small as in the tutorial since my computational
resources are limited, but when I tried running more precise sampling, the
results were pretty much the same (irregular courve).
Thanks in advance.
Przemek
part of md_umbrella.mdp:
; Run parameters
integrator = md
dt = 0.004
tinit = 0
nsteps = 2500000 ; 10 ns
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
--
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
