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

[Justin A. Lemkul]

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.

-Justin

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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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