[gmx-users] Simulation in vacuo

berka at natur.cuni.cz berka at natur.cuni.cz
Wed Nov 30 09:55:13 CET 2005

Hello GMXers,

i want to relax my transmembrane protein, so I thought, that it can be 
done in vacuo for some ps.

But I had some troubles with packing of protein, so id like to know 
which parameters are reasonable for this kind of simulation.

Firstly I want to know if it is ok, when I turn off pressure coupling?

Secondly, my protein isn't neutral, so I'd like to change PME for long 
Cut-off. I have found, that for that case I should take all *list = 0, 
but simulation can't be started. Have I missed something?

Thirdly I have more general question: Are there any standard .mdp 
settings which works in certain cases? (i.e. in water, in vacuo, with 
lipid bilayer, etc.) It could help newbies like me. And when they will 
be explained, it could be even better.

Karel Berka
undergraduate student of Charles University in Prague, Czech Republic

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