[gmx-users] pca on amber MD output

[Mark Abraham]

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