Hi, If it's the same protein you can extract the trajectories with the coordinates of the protein only using trjconv.
Ran. Afonso Duarte wrote: > Hi to All, > > I have some simulations of the same protein in different solvents, > with different number of atoms for each (different solvent number of > atoms). > I would like to calculate a rmsd matrix to compar the backbone of the > different sims. > > I have tried g_rms with the -f2 option to include the second > trajectory, however it finishes with a fatal error because teh number > of total atoms is different in both trajectories. > > Does anybody know how to solve this question? Is it possible to > produce the rmsd matrix in a different way? > > Thanks in advance > > Afonso > > __________________________________________________ > Fale com seus amigos de graça com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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