[gmx-users] problem in bilayer simulation

[pragya chohan]

> 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: mark.abraham at anu.edu.au
> To: gmx-users at gromacs.org
> 
> >
> >
> > 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
> 
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