[gmx-users] united atoms membranes & timestep

David Bostick dbostick at email.unc.edu
Tue Jan 7 16:42:21 CET 2003


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.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Tue, 7 Jan 2003, 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.
> Thanks in advance for any help.;-)
> John ;-)
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