On 11/26/12 1:03 AM, ramesh cheerla wrote:
Dear Gromacs users,
I am calculating PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations have pullaed pulled the adjacent ions to the vacant binding
site (tunnel is aligned along Y- axis).
for this I have used the following options in .mdp file.
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N Y N
pull_start = yes
pull_ngroups = 1
pull_group0 = REFA
pull_rate1 = 0.01
pull_k1 = 3000 ; kJ mol^-1 nm^-2
Here pull_group0 = REFA is the ion at another binding site and
pull_group1 = ATBP is the atom that I am pulling to the vacant site.
In next step I have performed umbrella sampling simulations to the selected
configurations using the following options :
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N Y N
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = REFA
pull_group1 = ATBP
pull_init1 = 0
pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000 ; kJ mol^-1 nm^-2
pull_nstxout = 100
pull_nstfout = 100
After that I have constructed PMF profile using Gromacs tool "g_wham",
while using g_wham I am getting the following warnings,
"WARNING, no data point in bin 34 (z=0.889382) !
You may not get a reasonable profile. Check your histograms!"
I have checked my histograms instead of one histogram for each
configuration with perfect overlapping, I am getting only one histogram.
You're probably just plotting the file wrong.
xmgrace -nxy histo.xvg
Here I am sending the link that containing PMF profile and histogram that
have obtained.
http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg
http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg
The PMF suggests massive undersampling (or complete lack of sampling) in several
areas.
the weired thing that I have observed in my pulling simulations is that I
have expected motion of ion in positive Y-direction for my pull parameters
but it is moving in negative Y- direction.
Can anybody please suggest me a solution for this, Am I following correct
protocol to get PMF of my system, is there any better method that suits for
my system.
If you are trying to see a complete translocation of an ion through a channel,
the "distance" geometry is inappropriate, as it does not deal correctly with the
change of sign for the vector between the reference and pulled group, IIRC. Try
"position" geometry and associated settings.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
