[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
reach.anirban.ghosh at gmail.com
Fri Apr 27 16:24:24 CEST 2012
On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> On 4/27/12 10:00 AM, Bala S wrote:
>> 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
> Yes, as Justin mentioned, the equilibration runs (restraining the
protein) will fill those gaps.
> 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
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users