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

Justin A. Lemkul jalemkul at vt.edu
Fri May 1 03:08:14 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?

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?

> 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.


> Any suggestions?
> Heiko
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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