[gmx-users] NMA in vaccum or water?

[Bert de Groot]

Ruben Martinez Buey wrote:
> 
> One question more: should I include counter-ions if the protein is charged??

good question. Probably there are pro's and cons. Including them would be
more realistic (since there will be counter ions around somehwere). But
the "somewhere" is the problem. Unlike in MD, where ions can float around,
in NM you'd have to choose a fixed position for them, which might result in
weird artefacts, especially if you choose unrealistic positions. So unless 
you have a good idea on where to put them, it might be better to leave them out.

But if you can afford the time: please do the comparison with/without
and report back to the list!

> What would be the .mdp input for generate the .tpr for genion?

a usual em-style mdp should do.

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________