On Tue, 11 Jul 2006, merc mertens wrote: >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.
you do need this option (-demux) and the xvg file should hold N+1 columns containing the correct permutation of replicas, e.g. time repl 0 1 2 3 ... 0 0 1 2 3 1 1 0 2 3 2 1 2 0 3 and so on > > >-------- Original-Nachricht -------- >Datum: Tue, 11 Jul 2006 15:05:04 +0200 >Von: Xavier Periole <[EMAIL PROTECTED]> >An: Discussion list for GROMACS users <[email protected]> >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 [email protected] >> 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://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] 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
