[gmx-users] coarse grain lipid and protein

[Erik Lindahl]

Hi,

Unfortunately it's not that simple. Protein structure is much more  
ordered than lipids, and very dependent on hydrogen bond patterns and  
other specific interactions. Thus, it not straightforward (and  
probably not even possible) to just replace e.g. an entire residue  
with a single interaction site and hope to get reasonable results.

You might be able to use a two-tiered approach with coarser  
interactions between lipid-protein, and finer inside the protein, but  
for large proteins you would then still need to use normal-length  
(2fs) timesteps.

Cheers,

Erik


On Jan 2, 2006, at 11:18 AM, John Simms wrote:

> Hi All,
> Just wondering whether anyone has extended Marrink's superb CG  
> lipid forcefield to include parameters/residue entries for proteins?
> Cheers John
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060102/48a201a6/attachment.html>