[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Peter C. Lai]

Looks I got to the party late (at a conference with limited time to do emails).

As a shameless self-plug, we recently published a soup-to-nuts protocol paper
for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF.

Our timescales are on the order 100+ns.

20ns/day is possible on 100K atoms with around 200 xeon x5650 cores over
qdr infiniband (4-order PME with 1.2nm cutoffs 0.16 fourier spacing, vdwtype 
switch=0.8 and h-bond LINCS with 0.002ps dt).

http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract

On 2012-04-26 01:40:17PM -0400, Justin A. Lemkul wrote:
> 
> 
> On 4/26/12 9:35 AM, Bala S wrote:
> > Dear Anirban,
> >
> > Thanks for the tutorial you have created for the newbies like me to follow.
> >
> > I wonder the tutorial is only for the GPCRs not applicable for other
> > membrane proteins?
> >
> 
> Tutorials present possible workflows.  Anirban's tutorial does not significantly 
> differ from my own (linked from his) which I happen to know has been applied to 
> many different systems.  There is nothing GPCR-specific in this new tutorial, 
> just like there is nothing KALP-specific about mine.
> 
> > I also have another question about slecting a lipidbilayer, what is the
> > criteria is selecting it, for instance popc, dopc or dppc?
> >
> 
> The choice of lipid depends on what you need to model.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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Peter C. Lai			| University of Alabama-Birmingham
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