[gmx-users] Simulation in vacuo

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 30 11:40:09 CET 2005

berka at natur.cuni.cz wrote:
> 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.
Is it the protein you want to relax or lipids?
Either way start with position restraints and a short cutoff, of e.g. 1 nm.
> Firstly I want to know if it is ok, when I turn off pressure coupling?
you must in vacuo.

> 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?
All cutoffs to zero means infinite cutoff.

> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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