[gmx-users] Umbrella_pull_simulation

[Justin A. Lemkul]

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 <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
> 
>     -- 
>     ==============================__==========
> 
>     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

========================================