[gmx-users] united atoms membranes & timestep

[Anton Feenstra]

J Simms wrote:
> 
> Hi All,
>         Hope everyone had a Good New Year. Just a quick question, I
> just wondered how high a timestep I can get away with using a
> united atom lipid forcefield?? Does anyone have any experience
> with this. The reason I want to find out, is that I have got a
> membrane protein that I want to use dummy atoms & heavy
> hydrogens with so that I can increase the timestep as with Antons
> papers. Can I increase the timestep and keep a well defined
> membrane or do I have to add the bilayer to the .rtp file and get
> pdb2gmx to deal with it.

Something else that just occurred to me: you can of course test
energy conservation for your lipids as a function of timestep.
As a good measure for energy conservation, you need the RMS drift
of the energy over a number of simulations, e.g. 10 times 10 ps
should be sufficient (detailed description in my paper, references
also of A.K. Mazur). You can take a very small system, e.g. 10-20
lipids and no water for this. It depends on the objectives of your
simulations, and a bit on personal taste, where you want to take
a cut-off on the acceptable level of energy drift.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "The World is a Friendly Place" (Magnapop)                |
|________|___________________________________________________________|