hm, i want to produce one continuous trajectory from several trajectories, that are output from a REMD run. i could not find much information about this matter, but from what i read i gathered that one needs to reorder all the trajectories into a new one using the demux option in trjcat. as far as i understand it, the remd.xvg should contain the information on the replica exchanges to reconstruct their walk through the different trajectories (i.e. the temperature space). but then i might be totally wrong. i have to admit, that somehow i got a bit lost between the concept of a continuous trajectory from REMD simulations and the walk through temperature space of the single replicas. further, i simply do not understand the format of remd.xvg that is shown by trjcat -h. thanks for any help.
-------- Original-Nachricht -------- Datum: Tue, 11 Jul 2006 15:05:04 +0200 Von: Xavier Periole <[EMAIL PROTECTED]> An: Discussion list for GROMACS users <gmx-users@gromacs.org> Betreff: Re: [gmx-users] REMD > > >at the end of a REMD run in gromacs I have as many trajectories as > replicas used for simulation. To produce one continuous trajectory trjcat was > recommended in a previous message. Since it neither makes sense to simply > concatenate all trajectories nor can one sort them by time, I suspect that one > needs to use the demux option in trjcat. Is that true? And if so, could > someone explain how this option works, because from the manual I could not > figure out how the necessary xvg should look like. > > > > > it is not clear what you actually want to do and the trjcat -h > indicates the format for remd.xvg > > XAvier > > -- > ---------------------------------- > Xavier Periole - Ph.D. > > Dept. of Biophysical Chemistry / MD Group > Univ. of Groningen > Nijenborgh 4 > 9747 AG Groningen > The Netherlands > > Tel: +31-503634329 > Fax: +31-503634398 > email: [EMAIL PROTECTED] > web-page: http://md.chem.rug.nl/~periole > ---------------------------------- > > _______________________________________________ > 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 -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer _______________________________________________ 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
