Hi Mark, Thank you very much for the clarification. I am also testing this at the moment running with and without Anstroms/nm conversions.
Regards, Nadia Quoting Mark Abraham <[EMAIL PROTECTED]>: > [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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
