Hi, Thank you for your reply.
Regards, Nadia Vahdati Quoting David van der Spoel <[EMAIL PROTECTED]>: > [EMAIL PROTECTED] wrote: > > Hi gromacs users, > > > > Recently I asked about running PCA on MD output from Amber which was > > helpful. Based on the advise I used g_covar to run PCA on all atoms. > > When I look at my average structure or filtered trajectory, I notice > that > > some of the bonds are much shorter than expected, and in the case of > NH3 or > > Hydrogens bound to C or N the bonds are even shorter, making the H's on > the > > NH3 group to ready bunch up together. > > > > for example for Lysine the bond between CD and CE are reduced from 1.53 > > Angstroms to 0.79 and for CE to HE2 from 1.00 to 0.49 and for NZ to HZ2 > in > > the NH3, from 1.00 to 0.28 > > > > Is the average structure a true Cartesian average? > > > yes, therefore you can expect it to be non-physical. > > > > Thank you in advance. > > > > Nadia Vahdati > > > > J.W.Essex group > > University of Southampton > > UK. > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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 > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > 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
