[gmx-users] pca on amber MD output

nadiav at soton.ac.uk nadiav at soton.ac.uk
Fri Oct 6 10:54:04 CEST 2006

Hi Mark,

Thank you very much for the clarification.  I am also testing this at the
moment running with and without Anstroms/nm conversions.



Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> nadiav at soton.ac.uk wrote:
> > Hi gromacs users,
> >
> > I am a new user to gromacs and realise that there are lots of comments
> on
> > the archive already about using gromacs with amber outputs but I am
> getting
> > rather mixed messages.
> >
> > I would like to clarify a few things.  I have an Amber trjectory file
> saved
> > through VMD in a .pdb format and a pdb file for the topology.
> >
> > I see that some say that one should convert the trajectory file, some
> say
> > that gromacs reads .pdb and others mention changing the extension to
> .g87
> > and so on.  My main question is about the fact that amber works in
> > Angstroms and gromacs in nm.  Should I convert my trajectory.pdb and
> > topology.pdb to nm before carrying out principal component analysis?
> There would be no need, since PCA is scale-independent. Further, the PDB
> format prescribes the use of Angstroms, so I expect any software to
> presume the use of Angstroms in any PDB file (since they can't tell the
> point of origin of the PDB file). You could, of course, test this
> yourself.
> Mark
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