[gmx-users] image control
myunggi at gmail.com
Wed Jan 16 00:01:09 CET 2008
I know general setup to run a simulation, and I'm running one.
As you see the title, I have problem with image.
I'm getting broken lipid in the trajectory.
Would you let me know how to avoid this?
Do I need special setup?
On Jan 15, 2008 5:30 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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