On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > On 4/27/12 10:00 AM, Bala S wrote: > >> Anirban, >> >> Exactly.. That's the gap (either side of the leaflets) I was mentioning >> about. I'll try EM and check itagain. >> >> > EM won't fill in solvent gaps. If you're using my protocol for increasing > the C radius in vdwradii.dat, then a small gap is normal and will close > when doing equilibration as the solvent fills in around the lipid > headgroups. > > Yes, as Justin mentioned, the equilibration runs (restraining the protein) will fill those gaps. Anirban -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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