On 5/21/12 10:05 AM, Du Jiangfeng (BIOCH) wrote:
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On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on Justin's tutorial, with the
sample spacing of 0.2 nm.
Can you provide images of what your histograms and PMF profile look like?
What energetic term is this? A summation can decrease if the values being added
are all negative.
The energetic term should be binding energy.
Even there are some samples with the negative energies but the energy curve
shouldn't go to zero (I calculated them by hand).
I don't understand what this means. Binding energy is not stored in the .edr
file, and I'm not clear what you calculated yourself.
Followings are some lines from the end of histograph file:
Distance(nm) 5.455761 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
8 5.483663 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0
0 0 0 8 5.511565 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 12
5.539467 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
4 5.567369 0 0 0 0 0 0 0 0
0 0
0 0 0 0 0 0 0 0 2
I am really depressed because it took me quiet a long time to sampling but it
seems in vain... I really no idea to find out what went wrong.
Nor do we. What is in your .mdp file? How many windows are you using? What is
the total desired length of the reaction coordinate, and what are the initial
and final COM distances that you are restraining? What are your box dimensions?
-Justin
My box dimensions are x: 7.94677 y: 7.94677 z: 13.48094 (nm)
The initial COM of DOPC(lipids) is at z=3.5 nm;
The initial COM of my protein is at z= 6.65nm.
The desired length is 3.6 nm, but it moved 3.4 nm along z-dimension.
So I used 19 windows for 3.4 nm movement (0.17 nm / window)
In pulling.mdp:
dt= 2 fs; nsteps=1 ns; nstxout=10 ps; nstvout=10ps
rlist/rcoulomb/ rvdw= 1.4
Tcoupl= v-rescale; Pcoupl= Parrinello-Rahman
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance> 0
pull_ngroups = 1
pull_group0 = DOPC
pull_group1 = protein
pull_rate1 = 0.0036 ; 0.0036 nm per ps = 3.6 nm per ns
pull_k1 = 1300 ; kJ mol^-1 nm^-2
In umbrella sampling.mdp:
nsteps=9.5 ns; pull_rate1= 0.0; pull_k1= 1000
other parameters are same as pulling.mdp.
Thank you for your help, above are my parameters.
In principle, this setup should work fine. What does grompp say about the
restrained distances? Does it agree with what you've calculated above in terms
of COM distances?
-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
========================================
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