[EMAIL PROTECTED] 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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