[gmx-users] abnormal RMSD

[Tsjerk Wassenaar]

Hi,

You may have written only a subset of atoms to the new trajectory
files using trjconv. Keep track of what you're doing and what is in
which file. Besides, most analysis tools also accept .pdb/.gro files
for reference.

Cheers,

Tsjerk

On Feb 15, 2008 6:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> > " Molecule in topology has atom numbers below and above natoms. you are
> > probably trying to use a trajectory which does not match the first 330 atoms
> > of the run input file. You can make a matching run input file with tpbconv."
>
> Use the same .tpr file that you submitted to mdrun to generate the trajectory.
> It has the reference structure for your simulation (t=0).  Try with -pbc nojump
> and -pbc whole to see which reconstructs your system appropriately.
>
> -Justin
>
> >
> > with regards
> >  Anamika
> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623