[gmx-users] On the use of SD and CG

Anton Feenstra feenstra at chem.vu.nl
Tue Nov 18 09:15:02 CET 2003

Martina Bertsch, PhD wrote:

> I have a feeling this adventure should not be quite so eventful: I am 
> getting every single error message from the book. Any kind suggestions?

I know from many of my 'membrane' coleagues, that the initial setting up
of a protein-membrane-solvent system often is dauntingly eventful, if that
may be of any comfort to you... ;-)

Now for some practical advice I can offer you at this point. Firstly,
after adding the ions you basically have a completely new system, for
which you will have to start right back at square '1' with (cycles of)
EM (SD or CG or both). Also, it may help to do the EM in steps, like
first EM protein in vacuum, then add bilayer, EM protein + bilayer, add
water, EM whole system, add ions, EM system+ions (and, of course, if
you are going to MD with PME, also EM with PME). The worst part, so
I hear, is the protein-bilayer interface, so it may help to equilibrate
that a bit before adding water, e.g. by posre on the protein and on
the bilayer normal axis (probably Z coordinate). Don't know if this
works in practice, but it sounds similar to things I've heard from the
guys that actually work with membranes.

P.S., thanks for your kind acknowledgements, and also for reminding
me why I work with soluble proteins... ;-)


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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