xi zhao wrote: > I performed remd using GROMACS 3.3.1 at four different temperatures: > 270k, 400k, 540k, 660k, and produced four trajectories. I want to know > whether my simulation is ok, but I do not know how to analysis my > trajectories. Though I have demux.pl script and produced > replica_index.xvg and replica_temp.xvg files, the contents of two files > are the same! I use trjcat_d to produce a continuous > trajectory,according to wiki gromacs. In fact, for a REMD > simulation, I can not judge whether the simulations is ok , and if they > are ok, how to further analyze or extract useful information from > trajectories! Are you clear? > Thank you for your help!
read your output file (md.log). view the xvg files. then come back with more directed questions. > > */Mark Abraham <[EMAIL PROTECTED]>/* 写道： > > xi zhao wrote: > > Dear all users: > > I performed remd using GROMACS 3.3.1,but I find that I do not > know how > > to analyze the result further, > > "Analyze" really doesn't tell us what you're trying to do. > > > though I have demux.pl script and produced > > replica_index.xvg and replica_temp.xvg files, the contents of two > files > > are the same! I use trjcat_d to produce a continuous trajectory,when > > analyzing the trajectory, the system shows segment fault? Please > give me > > some advice and analysis tools! > > You need to tell us what you're trying to do explicitly. That means text > describing your intentions, a command line that you tried to use, the > output from it, and (potentially) why you think it wasn't what you > expected. > > A segmentation fault is a generic problem with referencing an illegal > memory location, and thus just about anything could cause it. If there's > no GROMACS-specific error message, though, then it's very likely to be > something you've done wrongly. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > > > > > > 4 > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 > > > > > 雅虎邮箱，您的终生邮箱！ <http://cn.mail.yahoo.com/> > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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
