Re: [gmx-users] configuration does not change in minimization trajectory

[heiko252 at web.de]

> >> heiko252 at web.de wrote:
> >>> Hello all,
> >>>
> >>> I am doing a cg minimization with Gromacs-4.0.3.
> >>> It is compiled on a Linux system with gcc 3.4.6
> >>>
> >>> All frames in the trajectory are identical to the starting configuration,
> >>> except for the final one, which is clearly different.
> >>>
> >> How are you assessing this?  External viewing programs don't always show the 
> >> necessary level of detail.  If you use trjconv -dump to drop out a few select 
> >> frames, and diff the resulting .gro files, are they indeed identical, or are 
> >> there small differences?
> >>
> > All configurations but the last one are strictly identical to the first.
> > (Determined as suggested, using diff on .gro files dumped from the trajectory)
> > 
> 
> I see something similar with my own CG trajectories.  I do not routinely inspect 
> them; I typically rely on the energy curve and final output structure to 
> determine the adequacy of the procedure.
> 
> What I find in my own case is that the third decimal differs by no more than 1 
> unit between the reference structure and the constituent frames of the .trr 
> file.  It would seem to me that if you are seeing no difference along the 
> different frames, this is probably just a machine precision issue.
> 
> Differences are more obvious, however, when using steepest descents, and the 
> trajectory, when viewed in VMD, shows continual change in the structure.
> 
> >> How different is the final structure?  Is there a drastic change?  Or is it just 
> >> that the change relative to the input structure is more obvious?
> >>
> > The rmsd between the first and last structures is about 0.1 nm,
> > using -nomw with g_rms. So any changes to the structure are local, but obvious in VMD.
> > 
> 
> I would think that 0.1 nm is somewhat large for a simple minimization procedure, 
> although this is probably dependent upon system size and which components you 
> are analyzing.
> 
> -Justin
> 
> >>> I get the expected number of frames in the trajectory (.trr),
> >>> and the energy saved in the .edr is decreasing.
> >>> But apparently the changes in the structure do not reach the trajectory file.
> >>>
> >> If the energy is changing, then so too should the structure.
> >>
> > I agree, internally the structure must be changing, only the output does not show it.
> > 
> >> -Justin
> >>
> >>> Any suggestions?
> >>>
> >>> Heiko
> >>>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > 
> > Thanks for your input,
> > 
> > Heiko

I found the likely cause in the source and have submitted a bug report (# 321).
My impression is that the minimization itself is not affected.

-Heiko

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