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

heiko252 at heiko252 at
Sat May 2 01:37:41 CEST 2009

> -----Ursprüngliche Nachricht-----
> Von: "Justin A. Lemkul" <jalemkul at>
> Gesendet: 01.05.09 03:10:01
> An: Discussion list for GROMACS users <gmx-users at>
> Betreff: Re: [gmx-users] configuration does not change in minimization trajectory

> heiko252 at 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)

> 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 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] | (540) 231-9080

Thanks for your input,


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