Re: [gmx-users] configuration does not change in minimization trajectory
heiko252 at web.de
heiko252 at web.de
Tue May 5 04:44:39 CEST 2009
> >> 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.
> >>> 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.
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