[gmx-users] problem in bilayer simulation

[Mark Abraham]

pragya chohan wrote:
> 
>> 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.

Try it and some alternatives and see what works.

Mark