Hi Roy,
> i was wondering if Amber11 is able to support lipid bilayer simulation
> with
> a protein embedded in it? Anybody have tried it before and have any
> feedbacks on it? This is because i find most lipid bilayer simulation
> is
> performed on Gromacs instead.
In principal yes assuming you have an initial starting structure. AMBER's
support for lipids has not traditionally been very stellar although we are
trying to address this including new lipid force fields and also additional
traditionally used (but questionable???) features such as constant surface
tension. Please stay tuned. For the moment though you could certainly setup
and run a lipid bilayer simulation in AMBER. Indeed if you build it with
CHARMM and use the CHARMM force field (and or the charmm lipid builder) you
can use Chamber to run in either Sander or PMEMD and on GPUs if you want.
Good luck,
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Jul 06 2011 - 08:30:04 PDT
