> I understood that it is a periodic boundry condition problem and used > trjconv. But it writes a trajectory file. How do I make a gro file to > input it into next run Thanks I guess I was wrong. trjconv does write gro files. In any case, working out > how to do the restart is totally separate from any post-processing you've > done for visualization purposes. Ya i want to post process my file and not restart it. I am using the command trjconv -f md.gro -pbc inbox -center rect -o processed.gro I have gromacs 3.3.1 version. Am I using the correct command. I want to put all the water displaced back so that my initial rectangular structure is conserved. ---------------------------------------- > Date: Tue, 1 Jan 2008 14:41:09 +1100 > Subject: RE: [gmx-users] problem in bilayer simulation > From: [EMAIL PROTECTED] > To: [email protected] > > > > > > > I think you misunderstood my reply. > > I understood that it is a periodic boundry condition problem and used > > trjconv. But it writes a trajectory file. How do I make a gro file to > > input it into next run? > > Depending on what you're doing, you may not need one. See > http://wiki.gromacs.org/index.php/Doing_Restarts. In any case, working out > how to do the restart is totally separate from any post-processing you've > done for visualization purposes. > > > I cant even use tpbconv command because trjconv > > writes a xtc file and I need a trr file for my next run? > > First, trjconv will write whatever trajectory file format you ask for, and > this behaviour is common to all GROMACS tools. Second, you should be using > the .trr output of the last mdrun to prepare the input for the > continuations, and not the results of post-processing that output. > > Mark > > _______________________________________________ > 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
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