[gmx-users] problem in bilayer simulation

Mark Abraham mark.abraham at anu.edu.au
Tue Jan 1 04:41:09 CET 2008

> 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.


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