Thank you. 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 <[EMAIL PROTECTED]> 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. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Best wishes, MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
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