shahid nayeem wrote:
Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
-histo. But now as suggested by you I added -b 1000 -e 10000 leaving
1ns for equilibriation. The new profile.xvg is attached. How can I
further improve it.
I don't know. You've never even stated what your system is, how you decided on
the window spacing or time in each window, etc. It may be that your simulations
are too short. You have a few regions along the reaction coordinate that are
not well-sampled, which could contribute to some rockiness in the PMF.
-Justin
Shahid Nayeem
On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
I am attaching a profile.xvg and histo.xvg. In each window 10ns
sampling was done. The umbrella pullcode used is as follows.
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase pull_dim
= Y N Y
pull_vec1 = 0.75 0 1
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1
= 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
Please tell me my profile.xvg and histo.xvg are fine or not. In
profile.xvg why i am not getting smooth convergence.
They're not terrible, but could be better. The PMF profile is a
little rough and there are some regions of the reaction coordinate
with little sampling. Maybe your simulations need to be longer
and/or you need to exclude some amount of time at the beginning of
each as equilibration (which you probably should do anyway, but
without seeing your g_wham command, there's no way to know what you
may or may not be considering).
-Justin
Shahid Nayeem
On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
shahid nayeem wrote:
Thanks Justin
I have pulled one of the chain from an initial COM distance
value of 3.65 A to 7.90 A. When I look this trajectory in
VMD I
find that the
I will have to assume you mean nm. Gromacs does not deal in
Angstrom, and these distances would be within any sensible
short-range cutoff and thus not indicative of actual separation.
chain is completely separated. But even at this
separation the
profile.xvg file does not show its convergence to one
value. I
sent this file to you earlier.
Sorry, I don't have a photographic memory, nor can I recall if
you've ever posted your .mdp file, or at the very least, told
us how
much sampling you've done in each window. It may well be
that your
simulations are simply too short to observe adequate
post-equilibration sampling.
-Justin
-- ==============================____==========
Justin A. Lemkul
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Virginia Tech
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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