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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
