[gmx-users] united atoms membranes & timestep

[Anton Feenstra]

David Bostick wrote:
> 
> Hi!
> 
> Using LINCS, I can usually get a 4 fs timestep with a neat bilayer.
> Sometimes even with a simple protein in the membrane, I can still
> maintain a stable trajectory with 4 fs timestep without dummy atoms
> and heavy hydrogens.

That's also what Peter Tieleman did for his water channel (OMPF?)
in bilayer simulations, I mean take 4fs and no dummies. But IIRC he
did switch to using dummies when they became available. For a protein,
I'd say the abolute limit is 7 fs, above that you get numerous LINCS
warnings and frequent crashes.

Whether it is worthwile parsing the lipid topologies through pdb2gmx
depends mainly on how many (explicit) hydrogen atoms there are in the
lipids. I'd guess they are only in the headgroup and not many, so
you could get away by simply increasing their mass (be sure to subtract
the increase from the bonded heavy atom).


-- 
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)                |
|________|___________________________________________________________|