Syma Khalid wrote:
Hi Mark,
Firstly, thanks for your prompt response.
If they really are just counter-ions, then simple electrostatics will do
that... this is a side-issue, however.
Please can you explain the above?
If you take a point charge and a blob with opposite charge and do some
vacuum dynamics, they'll eventually stick together whether you use PBC
or not.
Will the ions simply collapse onto my
protein?
Don't know. The point is that they won't be moving like they're in a
medium with a substantial dielectric and viscous flow, as I was hinting
last email and David Mobley has now said.
The counter ions are simply to there to give me an overall neutral system.
Is there some other way I can get a neutral system?
That depends what physical question you are trying to answer with your
protein-without-solvent simulation. You might be better served
neutralizing the side chains by changing (e.g.) NH4+ to NH3, or doing
implicit solvent simulations without neutralizing, or getting solvent.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
