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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>> 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
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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========================================
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
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