[gmx-users] pca on amber MD output

nadiav at soton.ac.uk nadiav at soton.ac.uk
Thu Oct 5 16:56:53 CEST 2006

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?

I would be grateful for any comments.

Thank you in advance,

Nadia Vahdati

J.W.Essex group
University of Southampton

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