[gmx-users] image control

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 15 23:30:02 CET 2008

Myunggi Yi wrote:
> Thank you all of you.
> I've got a pre-equilibrated hydrated POPC bilayer from a web-site.
> I made a hole, and I placed my protein.
> Now, what is the next step?

If you're asking this, then you'll want to read most of the links from 
this site http://wiki.gromacs.org/index.php/Beginners, particularly the 
one listed under "S" :-)

Note also, that having a "pre-equilibrated" system in a .pdb file is not 
worth anything much. These don't come with velocities, and so you'd need 
to equilibrate them once you generate them. If you changed the box size 
and added more or less solvent, you'll need to equilibrate that. If 
you're worried about distorting the system during the equilibration, 
that's what position restraints are for. See man pdb2gmx, and chapters 4 
and 5 of the GROMACS manual.


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