Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 20 20:34:47 CET 2012
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).
> Shahid Nayeem
> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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 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
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users