Xavier, The output file of g_cluster with -dist option then gives the histogram of rmsd value distribution, is it? If it is the case, after plotting these data,I observe that the distribution resembles a gaussian type, its mean is located around 0.4 nm. This value is bigger compared to yours. Is it feasible? I performed my remd simulation in vacuum. It may be the reason?
-----Original Message----- From: "Xavier Periole" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Date: Tue, 12 Feb 2008 23:10:02 +0100 Subject: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option On Tue, 12 Feb 2008 23:55:35 +0200 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote: > Hi all, > > What does the second column of the output file of g_cluster with -dist >option stand for? Its title is a.u. I think it is atomic unit? In the manual, >it is not described. I believe a.u. stands for arbitrary unit. It should be the normalized distribution. You can check by integrating the curve ... should be one. XAvier > > Thanks in advance > Ozge Engin > ================================= > Computational Science & Engineering > Koc University > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 ----------------------------------------------------- XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole ----------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
